Starting phenix.real_space_refine on Thu Jul 31 21:44:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmj_61604/07_2025/9jmj_61604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmj_61604/07_2025/9jmj_61604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jmj_61604/07_2025/9jmj_61604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmj_61604/07_2025/9jmj_61604.map" model { file = "/net/cci-nas-00/data/ceres_data/9jmj_61604/07_2025/9jmj_61604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmj_61604/07_2025/9jmj_61604.cif" } resolution = 3.4 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= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8833 2.51 5 N 2235 2.21 5 O 2680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13813 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5963 Classifications: {'peptide': 728} Link IDs: {'PTRANS': 27, 'TRANS': 700} Chain: "C" Number of atoms: 5963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 728, 5963 Classifications: {'peptide': 728} Link IDs: {'PTRANS': 27, 'TRANS': 700} Chain: "B" Number of atoms: 1540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1540 Classifications: {'peptide': 200} Link IDs: {'PTRANS': 13, 'TRANS': 186} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} 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: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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: "H" 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: "I" 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: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.74, per 1000 atoms: 0.63 Number of scatterers: 13813 At special positions: 0 Unit cell: (133.32, 151.8, 89.76, 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 65 16.00 O 2680 8.00 N 2235 7.00 C 8833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 328 " - pdb=" SG CYS A 339 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 394 " distance=2.04 Simple disulfide: pdb=" SG CYS A 444 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 454 " - pdb=" SG CYS A 472 " distance=2.03 Simple disulfide: pdb=" SG CYS A 649 " - pdb=" SG CYS A 762 " distance=2.03 Simple disulfide: pdb=" SG CYS C 328 " - pdb=" SG CYS C 339 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 444 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS C 454 " - pdb=" SG CYS C 472 " distance=2.03 Simple disulfide: pdb=" SG CYS C 649 " - pdb=" SG CYS C 762 " distance=2.03 Simple disulfide: pdb=" SG CYS B 429 " - pdb=" SG CYS B 482 " distance=2.01 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 589 " distance=2.03 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 530 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A1101 " - " ASN A 92 " " NAG A1102 " - " ASN A 85 " " NAG A1103 " - " ASN A 150 " " NAG A1104 " - " ASN A 685 " " NAG C1101 " - " ASN C 92 " " NAG C1102 " - " ASN C 85 " " NAG C1103 " - " ASN C 685 " " NAG C1104 " - " ASN C 150 " " NAG D 1 " - " ASN A 321 " " NAG E 1 " - " ASN A 229 " " NAG F 1 " - " ASN A 219 " " NAG G 1 " - " ASN A 281 " " NAG H 1 " - " ASN C 219 " " NAG I 1 " - " ASN C 229 " " NAG J 1 " - " ASN C 281 " " NAG K 1 " - " ASN C 321 " Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 2.0 seconds 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 27 sheets defined 19.3% alpha, 32.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 92 through 97 removed outlier: 3.943A pdb=" N ASP A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 92 through 97' Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 421 through 425 removed outlier: 3.611A pdb=" N MET A 425 " --> pdb=" O TYR A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'A' and resid 562 through 570 Processing helix chain 'A' and resid 587 through 592 Processing helix chain 'A' and resid 593 through 595 No H-bonds generated for 'chain 'A' and resid 593 through 595' Processing helix chain 'A' and resid 601 through 615 Processing helix chain 'A' and resid 630 through 642 Processing helix chain 'A' and resid 663 through 671 removed outlier: 3.767A pdb=" N TYR A 670 " --> pdb=" O TYR A 666 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 Processing helix chain 'A' and resid 688 through 698 removed outlier: 3.687A pdb=" N ALA A 692 " --> pdb=" O MET A 689 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N GLU A 693 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN A 694 " --> pdb=" O ARG A 691 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 696 " --> pdb=" O GLU A 693 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN A 697 " --> pdb=" O ASN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 removed outlier: 4.339A pdb=" N SER A 716 " --> pdb=" O HIS A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 764 Processing helix chain 'C' and resid 44 through 50 Processing helix chain 'C' and resid 91 through 98 removed outlier: 4.177A pdb=" N PHE C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 206 Processing helix chain 'C' and resid 421 through 425 Processing helix chain 'C' and resid 497 through 504 Processing helix chain 'C' and resid 562 through 570 Processing helix chain 'C' and resid 587 through 592 Processing helix chain 'C' and resid 593 through 595 No H-bonds generated for 'chain 'C' and resid 593 through 595' Processing helix chain 'C' and resid 600 through 617 removed outlier: 4.181A pdb=" N GLY C 617 " --> pdb=" O PHE C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 641 Processing helix chain 'C' and resid 663 through 672 removed outlier: 3.833A pdb=" N TYR C 670 " --> pdb=" O TYR C 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 686 Processing helix chain 'C' and resid 688 through 698 removed outlier: 3.724A pdb=" N ALA C 692 " --> pdb=" O MET C 689 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLU C 693 " --> pdb=" O SER C 690 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN C 694 " --> pdb=" O ARG C 691 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 695 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS C 696 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN C 697 " --> pdb=" O ASN C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 712 through 727 removed outlier: 4.359A pdb=" N SER C 716 " --> pdb=" O HIS C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 744 through 763 Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.595A pdb=" N LEU B 393 " --> pdb=" O THR B 390 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 394 " --> pdb=" O LYS B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 390 through 394' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 434 through 439 Processing helix chain 'B' and resid 466 through 471 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 3.610A pdb=" N ARG A 61 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 104 through 107 removed outlier: 3.697A pdb=" N ASP A 104 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR A 120 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR A 129 " --> pdb=" O TYR A 120 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE A 134 " --> pdb=" O ILE A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 154 through 157 removed outlier: 3.882A pdb=" N TRP A 154 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AA5, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AA6, first strand: chain 'A' and resid 235 through 240 removed outlier: 3.586A pdb=" N VAL A 254 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A 238 " --> pdb=" O VAL A 252 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 298 through 307 removed outlier: 6.718A pdb=" N GLN A 314 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL A 303 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER A 312 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP A 305 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ARG A 310 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR A 322 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 307 removed outlier: 6.718A pdb=" N GLN A 314 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N VAL A 303 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N SER A 312 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TRP A 305 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ARG A 310 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N TYR A 322 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 363 through 364 Processing sheet with id=AB1, first strand: chain 'A' and resid 404 through 410 removed outlier: 6.061A pdb=" N ILE A 407 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE A 418 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 409 " --> pdb=" O TYR A 416 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 457 through 461 removed outlier: 3.566A pdb=" N LEU A 479 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU A 482 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N VAL A 493 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N SER A 484 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU A 491 " --> pdb=" O SER A 484 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 514 through 517 removed outlier: 3.629A pdb=" N VAL A 575 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ALA A 576 " --> pdb=" O PRO A 541 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU A 543 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N PHE A 578 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N ASP A 545 " --> pdb=" O PHE A 578 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N TYR A 540 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ALA A 625 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 542 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N TRP A 627 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU A 544 " --> pdb=" O TRP A 627 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N TRP A 629 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL A 546 " --> pdb=" O TRP A 629 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N CYS A 649 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE A 624 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N ILE A 651 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 626 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N VAL A 653 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY A 628 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TYR A 700 " --> pdb=" O GLN A 731 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N MET A 733 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU A 702 " --> pdb=" O MET A 733 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N TYR A 735 " --> pdb=" O LEU A 702 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N HIS A 704 " --> pdb=" O TYR A 735 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 61 through 62 removed outlier: 3.607A pdb=" N LEU C 77 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL C 78 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER C 86 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 104 through 107 removed outlier: 4.028A pdb=" N ASP C 104 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N TYR C 120 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N THR C 129 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.698A pdb=" N TRP C 154 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 194 through 196 Processing sheet with id=AB8, first strand: chain 'C' and resid 194 through 196 Processing sheet with id=AB9, first strand: chain 'C' and resid 235 through 240 removed outlier: 3.518A pdb=" N TYR C 238 " --> pdb=" O VAL C 252 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 298 through 307 removed outlier: 6.944A pdb=" N GLN C 314 " --> pdb=" O CYS C 301 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL C 303 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER C 312 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N TRP C 305 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ARG C 310 " --> pdb=" O TRP C 305 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR C 322 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 298 through 307 removed outlier: 6.944A pdb=" N GLN C 314 " --> pdb=" O CYS C 301 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL C 303 " --> pdb=" O SER C 312 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N SER C 312 " --> pdb=" O VAL C 303 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N TRP C 305 " --> pdb=" O ARG C 310 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ARG C 310 " --> pdb=" O TRP C 305 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N TYR C 322 " --> pdb=" O ARG C 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 363 through 364 removed outlier: 3.620A pdb=" N PHE C 371 " --> pdb=" O PHE C 387 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 404 through 410 removed outlier: 6.643A pdb=" N ILE C 418 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ILE C 407 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N TYR C 416 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA C 409 " --> pdb=" O TYR C 414 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR C 414 " --> pdb=" O ALA C 409 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 457 through 461 removed outlier: 6.114A pdb=" N LEU C 482 " --> pdb=" O VAL C 493 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N VAL C 493 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 8.384A pdb=" N SER C 484 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU C 491 " --> pdb=" O SER C 484 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 511 through 518 removed outlier: 4.720A pdb=" N PHE C 578 " --> pdb=" O ASP C 545 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR C 540 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LYS C 622 " --> pdb=" O TYR C 540 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N LEU C 542 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE C 624 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU C 544 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ILE C 626 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N CYS C 649 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE C 624 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N ILE C 651 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE C 626 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL C 653 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLY C 628 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C 700 " --> pdb=" O GLN C 731 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N MET C 733 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU C 702 " --> pdb=" O MET C 733 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N TYR C 735 " --> pdb=" O LEU C 702 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N HIS C 704 " --> pdb=" O TYR C 735 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.942A pdb=" N ASN B 404 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B 449 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 406 " --> pdb=" O VAL B 447 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 444 " --> pdb=" O GLN B 580 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN B 580 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 404 through 407 removed outlier: 3.942A pdb=" N ASN B 404 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N TYR B 449 " --> pdb=" O ASN B 404 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 406 " --> pdb=" O VAL B 447 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 516 through 518 removed outlier: 5.569A pdb=" N SER B 501 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR B 565 " --> pdb=" O SER B 501 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ILE B 503 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER B 563 " --> pdb=" O ILE B 503 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP B 543 " --> pdb=" O GLY B 562 " (cutoff:3.500A) 439 hydrogen bonds defined for protein. 1209 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: 8.11 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3664 1.33 - 1.46: 3499 1.46 - 1.58: 6932 1.58 - 1.70: 0 1.70 - 1.83: 98 Bond restraints: 14193 Sorted by residual: bond pdb=" CA GLN B 551 " pdb=" C GLN B 551 " ideal model delta sigma weight residual 1.528 1.476 0.052 1.38e-02 5.25e+03 1.42e+01 bond pdb=" N GLN B 551 " pdb=" CA GLN B 551 " ideal model delta sigma weight residual 1.453 1.420 0.033 1.37e-02 5.33e+03 5.67e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.56e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.50e+00 bond pdb=" CA LEU B 552 " pdb=" C LEU B 552 " ideal model delta sigma weight residual 1.523 1.496 0.026 1.45e-02 4.76e+03 3.33e+00 ... (remaining 14188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 19001 2.22 - 4.44: 266 4.44 - 6.66: 24 6.66 - 8.88: 6 8.88 - 11.11: 3 Bond angle restraints: 19300 Sorted by residual: angle pdb=" N GLN B 551 " pdb=" CA GLN B 551 " pdb=" C GLN B 551 " ideal model delta sigma weight residual 110.41 99.30 11.11 1.23e+00 6.61e-01 8.15e+01 angle pdb=" N LEU B 552 " pdb=" CA LEU B 552 " pdb=" C LEU B 552 " ideal model delta sigma weight residual 113.23 106.33 6.90 1.22e+00 6.72e-01 3.20e+01 angle pdb=" C MET B 456 " pdb=" CA MET B 456 " pdb=" CB MET B 456 " ideal model delta sigma weight residual 110.62 115.89 -5.27 1.46e+00 4.69e-01 1.30e+01 angle pdb=" CA TYR C 128 " pdb=" CB TYR C 128 " pdb=" CG TYR C 128 " ideal model delta sigma weight residual 113.90 120.23 -6.33 1.80e+00 3.09e-01 1.24e+01 angle pdb=" CA ASN B 532 " pdb=" CB ASN B 532 " pdb=" CG ASN B 532 " ideal model delta sigma weight residual 112.60 115.83 -3.23 1.00e+00 1.00e+00 1.04e+01 ... (remaining 19295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.45: 7829 21.45 - 42.89: 667 42.89 - 64.34: 123 64.34 - 85.79: 22 85.79 - 107.23: 9 Dihedral angle restraints: 8650 sinusoidal: 3751 harmonic: 4899 Sorted by residual: dihedral pdb=" CB CYS A 385 " pdb=" SG CYS A 385 " pdb=" SG CYS A 394 " pdb=" CB CYS A 394 " ideal model delta sinusoidal sigma weight residual 93.00 16.51 76.49 1 1.00e+01 1.00e-02 7.36e+01 dihedral pdb=" CB CYS A 454 " pdb=" SG CYS A 454 " pdb=" SG CYS A 472 " pdb=" CB CYS A 472 " ideal model delta sinusoidal sigma weight residual -86.00 -27.43 -58.57 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CB CYS B 441 " pdb=" SG CYS B 441 " pdb=" SG CYS B 589 " pdb=" CB CYS B 589 " ideal model delta sinusoidal sigma weight residual -86.00 -35.51 -50.49 1 1.00e+01 1.00e-02 3.49e+01 ... (remaining 8647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1745 0.062 - 0.123: 348 0.123 - 0.185: 25 0.185 - 0.247: 3 0.247 - 0.308: 2 Chirality restraints: 2123 Sorted by residual: chirality pdb=" C2 NAG D 1 " pdb=" C1 NAG D 1 " pdb=" C3 NAG D 1 " pdb=" N2 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.49 -2.18 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" C5 BMA E 3 " pdb=" C4 BMA E 3 " pdb=" C6 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN C 219 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 2120 not shown) Planarity restraints: 2441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 675 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO C 676 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 676 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 676 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 675 " -0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO A 676 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 676 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 676 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 422 " -0.014 2.00e-02 2.50e+03 1.51e-02 4.59e+00 pdb=" CG TYR A 422 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR A 422 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 422 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR A 422 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 422 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A 422 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 422 " 0.002 2.00e-02 2.50e+03 ... (remaining 2438 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2230 2.77 - 3.30: 11984 3.30 - 3.83: 23484 3.83 - 4.37: 27587 4.37 - 4.90: 48038 Nonbonded interactions: 113323 Sorted by model distance: nonbonded pdb=" OH TYR A 422 " pdb=" OE2 GLU A 448 " model vdw 2.232 3.040 nonbonded pdb=" OE1 GLU A 82 " pdb=" OH TYR A 467 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A 248 " pdb=" O TYR C 256 " model vdw 2.297 3.040 nonbonded pdb=" O ASN A 562 " pdb=" OG1 THR A 565 " model vdw 2.306 3.040 nonbonded pdb=" OE1 GLU A 232 " pdb=" O6 NAG E 1 " model vdw 2.314 3.040 ... (remaining 113318 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 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 23.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 37.290 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 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 : 0.004 0.052 14231 Z= 0.184 Angle : 0.662 11.105 19401 Z= 0.353 Chirality : 0.048 0.308 2123 Planarity : 0.005 0.058 2425 Dihedral : 16.055 107.233 5487 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.20 % Allowed : 17.06 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.19), residues: 1646 helix: -0.60 (0.30), residues: 245 sheet: -0.27 (0.22), residues: 519 loop : -1.33 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 627 HIS 0.005 0.001 HIS C 754 PHE 0.024 0.001 PHE B 533 TYR 0.036 0.002 TYR A 422 ARG 0.015 0.001 ARG B 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00201 ( 16) link_NAG-ASN : angle 1.73267 ( 48) link_BETA1-4 : bond 0.00660 ( 9) link_BETA1-4 : angle 1.87046 ( 27) hydrogen bonds : bond 0.21095 ( 414) hydrogen bonds : angle 8.61465 ( 1209) SS BOND : bond 0.00568 ( 13) SS BOND : angle 1.46046 ( 26) covalent geometry : bond 0.00368 (14193) covalent geometry : angle 0.65260 (19300) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 1.713 Fit side-chains revert: symmetry clash REVERT: A 528 MET cc_start: 0.8565 (mtm) cc_final: 0.8248 (mtm) REVERT: B 429 CYS cc_start: 0.6533 (OUTLIER) cc_final: 0.5910 (p) REVERT: B 572 GLN cc_start: 0.6898 (mt0) cc_final: 0.5837 (tp40) outliers start: 3 outliers final: 0 residues processed: 88 average time/residue: 0.2850 time to fit residues: 39.8865 Evaluate side-chains 70 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 429 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 0.0060 chunk 66 optimal weight: 0.7980 chunk 128 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 95 optimal weight: 0.9990 chunk 148 optimal weight: 0.0020 overall best weight: 0.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 GLN A 712 HIS C 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.096977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.079796 restraints weight = 27438.237| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.91 r_work: 0.2962 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.0805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14231 Z= 0.095 Angle : 0.496 10.691 19401 Z= 0.259 Chirality : 0.043 0.235 2123 Planarity : 0.004 0.043 2425 Dihedral : 7.696 69.754 2364 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.62 % Allowed : 15.98 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.20), residues: 1646 helix: 0.15 (0.32), residues: 246 sheet: -0.24 (0.22), residues: 532 loop : -1.08 (0.20), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 157 HIS 0.003 0.001 HIS C 748 PHE 0.014 0.001 PHE A 371 TYR 0.016 0.001 TYR B 459 ARG 0.004 0.000 ARG B 405 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 16) link_NAG-ASN : angle 1.56936 ( 48) link_BETA1-4 : bond 0.00412 ( 9) link_BETA1-4 : angle 1.52415 ( 27) hydrogen bonds : bond 0.03841 ( 414) hydrogen bonds : angle 5.86243 ( 1209) SS BOND : bond 0.00253 ( 13) SS BOND : angle 0.84586 ( 26) covalent geometry : bond 0.00196 (14193) covalent geometry : angle 0.48721 (19300) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 2.478 Fit side-chains revert: symmetry clash REVERT: A 157 TRP cc_start: 0.8762 (m100) cc_final: 0.8421 (m100) REVERT: A 162 HIS cc_start: 0.8554 (OUTLIER) cc_final: 0.7339 (p-80) REVERT: A 528 MET cc_start: 0.8516 (mtm) cc_final: 0.8183 (mtm) REVERT: C 310 ARG cc_start: 0.8368 (OUTLIER) cc_final: 0.8035 (ttp-110) REVERT: C 715 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: B 429 CYS cc_start: 0.6325 (OUTLIER) cc_final: 0.5365 (p) REVERT: B 474 LYS cc_start: 0.7564 (ttmt) cc_final: 0.6716 (tppt) REVERT: B 507 SER cc_start: 0.8899 (p) cc_final: 0.8583 (t) REVERT: B 509 LEU cc_start: 0.8732 (mm) cc_final: 0.8412 (tp) REVERT: B 517 GLU cc_start: 0.7759 (tp30) cc_final: 0.6877 (tp30) REVERT: B 572 GLN cc_start: 0.6599 (mt0) cc_final: 0.5626 (tp40) outliers start: 24 outliers final: 10 residues processed: 103 average time/residue: 0.3090 time to fit residues: 50.3938 Evaluate side-chains 87 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 0.0050 chunk 96 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 157 optimal weight: 0.2980 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.096066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.078748 restraints weight = 27612.111| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.94 r_work: 0.2949 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14231 Z= 0.093 Angle : 0.470 9.856 19401 Z= 0.242 Chirality : 0.043 0.231 2123 Planarity : 0.003 0.040 2425 Dihedral : 6.396 58.274 2364 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.96 % Allowed : 16.59 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.20), residues: 1646 helix: 0.77 (0.34), residues: 234 sheet: -0.25 (0.22), residues: 524 loop : -1.00 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 157 HIS 0.003 0.001 HIS A 748 PHE 0.019 0.001 PHE B 403 TYR 0.015 0.001 TYR C 105 ARG 0.004 0.000 ARG A 140 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 16) link_NAG-ASN : angle 1.46652 ( 48) link_BETA1-4 : bond 0.00345 ( 9) link_BETA1-4 : angle 1.47188 ( 27) hydrogen bonds : bond 0.03327 ( 414) hydrogen bonds : angle 5.21002 ( 1209) SS BOND : bond 0.00189 ( 13) SS BOND : angle 0.63233 ( 26) covalent geometry : bond 0.00197 (14193) covalent geometry : angle 0.46155 (19300) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 3.284 Fit side-chains revert: symmetry clash REVERT: A 162 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.7259 (p-80) REVERT: C 715 GLN cc_start: 0.8787 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: B 429 CYS cc_start: 0.6361 (OUTLIER) cc_final: 0.5349 (p) REVERT: B 474 LYS cc_start: 0.7656 (ttmt) cc_final: 0.6978 (tppt) REVERT: B 507 SER cc_start: 0.8863 (p) cc_final: 0.8523 (t) REVERT: B 517 GLU cc_start: 0.7706 (tp30) cc_final: 0.6586 (tp30) REVERT: B 572 GLN cc_start: 0.6594 (mt0) cc_final: 0.5722 (tp40) outliers start: 29 outliers final: 17 residues processed: 106 average time/residue: 0.2566 time to fit residues: 44.4325 Evaluate side-chains 92 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 47 optimal weight: 0.9990 chunk 120 optimal weight: 0.0970 chunk 113 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 GLN C 508 GLN B 399 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.091990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.074651 restraints weight = 27875.122| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.92 r_work: 0.2876 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14231 Z= 0.174 Angle : 0.518 9.344 19401 Z= 0.268 Chirality : 0.044 0.229 2123 Planarity : 0.003 0.036 2425 Dihedral : 5.835 59.095 2364 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.76 % Allowed : 15.85 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.20), residues: 1646 helix: 0.86 (0.34), residues: 237 sheet: -0.35 (0.22), residues: 521 loop : -0.92 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 157 HIS 0.005 0.001 HIS C 483 PHE 0.018 0.001 PHE A 387 TYR 0.017 0.002 TYR B 459 ARG 0.003 0.000 ARG C 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00211 ( 16) link_NAG-ASN : angle 1.69807 ( 48) link_BETA1-4 : bond 0.00212 ( 9) link_BETA1-4 : angle 1.49418 ( 27) hydrogen bonds : bond 0.03503 ( 414) hydrogen bonds : angle 5.15587 ( 1209) SS BOND : bond 0.00182 ( 13) SS BOND : angle 0.79120 ( 26) covalent geometry : bond 0.00397 (14193) covalent geometry : angle 0.50847 (19300) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8668 (OUTLIER) cc_final: 0.8411 (mm-40) REVERT: A 715 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8024 (mt0) REVERT: C 557 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8762 (p) REVERT: C 715 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8323 (mt0) REVERT: B 429 CYS cc_start: 0.6492 (OUTLIER) cc_final: 0.5546 (p) REVERT: B 474 LYS cc_start: 0.7784 (ttmt) cc_final: 0.7499 (tppt) REVERT: B 507 SER cc_start: 0.8968 (p) cc_final: 0.8761 (p) REVERT: B 572 GLN cc_start: 0.6364 (OUTLIER) cc_final: 0.5482 (tp40) outliers start: 41 outliers final: 24 residues processed: 113 average time/residue: 0.2150 time to fit residues: 39.4945 Evaluate side-chains 104 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 675 THR Chi-restraints excluded: chain A residue 715 GLN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 458 SER Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 142 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 chunk 120 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.093357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.076130 restraints weight = 27900.937| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.92 r_work: 0.2898 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14231 Z= 0.101 Angle : 0.463 9.331 19401 Z= 0.240 Chirality : 0.043 0.230 2123 Planarity : 0.003 0.040 2425 Dihedral : 5.415 57.879 2364 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.43 % Allowed : 16.93 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.20), residues: 1646 helix: 1.00 (0.34), residues: 237 sheet: -0.34 (0.22), residues: 521 loop : -0.87 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 629 HIS 0.003 0.001 HIS C 748 PHE 0.016 0.001 PHE A 387 TYR 0.012 0.001 TYR C 752 ARG 0.002 0.000 ARG C 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 16) link_NAG-ASN : angle 1.53202 ( 48) link_BETA1-4 : bond 0.00291 ( 9) link_BETA1-4 : angle 1.29148 ( 27) hydrogen bonds : bond 0.03043 ( 414) hydrogen bonds : angle 4.93664 ( 1209) SS BOND : bond 0.00240 ( 13) SS BOND : angle 0.71346 ( 26) covalent geometry : bond 0.00226 (14193) covalent geometry : angle 0.45414 (19300) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 2.097 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8374 (mm-40) REVERT: A 162 HIS cc_start: 0.8689 (OUTLIER) cc_final: 0.7386 (p-80) REVERT: A 715 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7973 (mt0) REVERT: C 217 SER cc_start: 0.8712 (OUTLIER) cc_final: 0.8493 (m) REVERT: C 557 THR cc_start: 0.9025 (OUTLIER) cc_final: 0.8788 (p) REVERT: C 715 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8202 (mt0) REVERT: B 429 CYS cc_start: 0.6377 (OUTLIER) cc_final: 0.5443 (p) REVERT: B 474 LYS cc_start: 0.7754 (ttmt) cc_final: 0.7432 (tppt) REVERT: B 572 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.5516 (tp40) outliers start: 36 outliers final: 25 residues processed: 108 average time/residue: 0.2789 time to fit residues: 48.8550 Evaluate side-chains 106 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 73 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 715 GLN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 217 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 127 optimal weight: 0.0050 chunk 1 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 157 optimal weight: 7.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.093275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.076148 restraints weight = 28102.262| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.91 r_work: 0.2898 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 14231 Z= 0.100 Angle : 0.456 9.407 19401 Z= 0.237 Chirality : 0.043 0.229 2123 Planarity : 0.003 0.041 2425 Dihedral : 5.123 58.036 2364 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.90 % Allowed : 16.86 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.20), residues: 1646 helix: 1.04 (0.34), residues: 238 sheet: -0.36 (0.22), residues: 522 loop : -0.83 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 629 HIS 0.003 0.001 HIS A 748 PHE 0.015 0.001 PHE A 387 TYR 0.012 0.001 TYR C 752 ARG 0.002 0.000 ARG C 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 16) link_NAG-ASN : angle 1.50728 ( 48) link_BETA1-4 : bond 0.00274 ( 9) link_BETA1-4 : angle 1.24889 ( 27) hydrogen bonds : bond 0.02913 ( 414) hydrogen bonds : angle 4.82207 ( 1209) SS BOND : bond 0.00213 ( 13) SS BOND : angle 0.65567 ( 26) covalent geometry : bond 0.00225 (14193) covalent geometry : angle 0.44803 (19300) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8369 (mm-40) REVERT: A 162 HIS cc_start: 0.8714 (OUTLIER) cc_final: 0.7396 (p-80) REVERT: A 715 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8005 (mt0) REVERT: C 557 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8812 (p) REVERT: C 715 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8279 (mt0) REVERT: B 418 LEU cc_start: 0.7275 (pt) cc_final: 0.6159 (tt) REVERT: B 429 CYS cc_start: 0.6403 (OUTLIER) cc_final: 0.5531 (p) REVERT: B 474 LYS cc_start: 0.7784 (ttmt) cc_final: 0.7437 (tppt) REVERT: B 572 GLN cc_start: 0.6353 (OUTLIER) cc_final: 0.5880 (tp40) REVERT: B 573 MET cc_start: 0.7451 (mmm) cc_final: 0.6638 (tpp) REVERT: B 575 PHE cc_start: 0.7938 (m-10) cc_final: 0.7406 (m-10) outliers start: 43 outliers final: 27 residues processed: 115 average time/residue: 0.2262 time to fit residues: 42.2006 Evaluate side-chains 107 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 715 GLN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain B residue 396 THR Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 572 GLN Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 8.9990 chunk 21 optimal weight: 0.3980 chunk 51 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 84 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 483 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.090423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.073379 restraints weight = 28253.043| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 1.88 r_work: 0.2842 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14231 Z= 0.189 Angle : 0.529 9.289 19401 Z= 0.274 Chirality : 0.044 0.231 2123 Planarity : 0.003 0.039 2425 Dihedral : 5.379 59.685 2364 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.63 % Allowed : 17.33 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1646 helix: 0.52 (0.33), residues: 262 sheet: -0.44 (0.22), residues: 522 loop : -0.89 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 629 HIS 0.005 0.001 HIS C 483 PHE 0.017 0.001 PHE A 387 TYR 0.036 0.002 TYR B 459 ARG 0.003 0.000 ARG C 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 16) link_NAG-ASN : angle 1.79679 ( 48) link_BETA1-4 : bond 0.00205 ( 9) link_BETA1-4 : angle 1.37013 ( 27) hydrogen bonds : bond 0.03420 ( 414) hydrogen bonds : angle 5.01374 ( 1209) SS BOND : bond 0.00299 ( 13) SS BOND : angle 0.89327 ( 26) covalent geometry : bond 0.00442 (14193) covalent geometry : angle 0.51915 (19300) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 68 time to evaluate : 1.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8499 (mp10) REVERT: A 715 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8103 (mt0) REVERT: C 557 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8823 (p) REVERT: C 715 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8363 (mt0) REVERT: B 429 CYS cc_start: 0.6491 (OUTLIER) cc_final: 0.5699 (p) REVERT: B 460 MET cc_start: 0.7163 (ttp) cc_final: 0.6922 (ttp) REVERT: B 474 LYS cc_start: 0.7837 (ttmt) cc_final: 0.7557 (tppt) REVERT: B 572 GLN cc_start: 0.6215 (OUTLIER) cc_final: 0.5526 (tp40) outliers start: 39 outliers final: 28 residues processed: 104 average time/residue: 0.2439 time to fit residues: 39.8542 Evaluate side-chains 100 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 66 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 715 GLN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.073287 restraints weight = 28214.350| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.90 r_work: 0.2844 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14231 Z= 0.160 Angle : 0.504 9.217 19401 Z= 0.260 Chirality : 0.044 0.229 2123 Planarity : 0.003 0.040 2425 Dihedral : 5.287 59.101 2364 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.56 % Allowed : 17.06 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1646 helix: 0.53 (0.33), residues: 262 sheet: -0.45 (0.22), residues: 520 loop : -0.91 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 629 HIS 0.004 0.001 HIS C 483 PHE 0.016 0.001 PHE A 387 TYR 0.025 0.001 TYR B 459 ARG 0.003 0.000 ARG C 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 16) link_NAG-ASN : angle 1.77720 ( 48) link_BETA1-4 : bond 0.00223 ( 9) link_BETA1-4 : angle 1.26287 ( 27) hydrogen bonds : bond 0.03203 ( 414) hydrogen bonds : angle 4.98882 ( 1209) SS BOND : bond 0.00260 ( 13) SS BOND : angle 0.83879 ( 26) covalent geometry : bond 0.00373 (14193) covalent geometry : angle 0.49478 (19300) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 67 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8474 (mm-40) REVERT: A 262 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8784 (m) REVERT: A 452 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8108 (pm20) REVERT: A 715 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: C 557 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8855 (p) REVERT: C 715 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: B 429 CYS cc_start: 0.6557 (OUTLIER) cc_final: 0.6136 (p) REVERT: B 474 LYS cc_start: 0.7850 (ttmt) cc_final: 0.7553 (tppt) REVERT: B 572 GLN cc_start: 0.6349 (OUTLIER) cc_final: 0.5632 (tp40) outliers start: 38 outliers final: 27 residues processed: 101 average time/residue: 0.2816 time to fit residues: 46.0068 Evaluate side-chains 103 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 68 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 715 GLN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 112 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.090149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.073146 restraints weight = 28018.836| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.89 r_work: 0.2845 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14231 Z= 0.155 Angle : 0.506 9.254 19401 Z= 0.262 Chirality : 0.044 0.228 2123 Planarity : 0.003 0.041 2425 Dihedral : 5.234 58.880 2364 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.56 % Allowed : 17.19 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.20), residues: 1646 helix: 0.53 (0.33), residues: 262 sheet: -0.46 (0.22), residues: 534 loop : -0.88 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 629 HIS 0.004 0.001 HIS C 483 PHE 0.016 0.001 PHE A 516 TYR 0.028 0.001 TYR B 459 ARG 0.002 0.000 ARG C 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 16) link_NAG-ASN : angle 1.79969 ( 48) link_BETA1-4 : bond 0.00215 ( 9) link_BETA1-4 : angle 1.25001 ( 27) hydrogen bonds : bond 0.03231 ( 414) hydrogen bonds : angle 4.97207 ( 1209) SS BOND : bond 0.00247 ( 13) SS BOND : angle 0.84218 ( 26) covalent geometry : bond 0.00359 (14193) covalent geometry : angle 0.49586 (19300) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 1.617 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8477 (mp10) REVERT: A 162 HIS cc_start: 0.8787 (OUTLIER) cc_final: 0.7574 (p-80) REVERT: A 262 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8785 (m) REVERT: A 452 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8076 (pm20) REVERT: A 715 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8100 (mt0) REVERT: C 557 THR cc_start: 0.9127 (OUTLIER) cc_final: 0.8893 (p) REVERT: C 715 GLN cc_start: 0.9110 (OUTLIER) cc_final: 0.8315 (mt0) REVERT: B 429 CYS cc_start: 0.6611 (OUTLIER) cc_final: 0.6253 (p) REVERT: B 474 LYS cc_start: 0.7844 (ttmt) cc_final: 0.7512 (tppt) REVERT: B 572 GLN cc_start: 0.6455 (OUTLIER) cc_final: 0.5764 (tp40) outliers start: 38 outliers final: 28 residues processed: 99 average time/residue: 0.2210 time to fit residues: 35.2646 Evaluate side-chains 100 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 715 GLN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 12 optimal weight: 2.9990 chunk 154 optimal weight: 10.0000 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.089771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.072754 restraints weight = 28189.895| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.90 r_work: 0.2835 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14231 Z= 0.164 Angle : 0.514 9.291 19401 Z= 0.265 Chirality : 0.044 0.229 2123 Planarity : 0.003 0.041 2425 Dihedral : 5.278 58.573 2364 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.49 % Allowed : 17.53 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.20), residues: 1646 helix: 0.54 (0.33), residues: 262 sheet: -0.50 (0.22), residues: 542 loop : -0.89 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 629 HIS 0.004 0.001 HIS C 748 PHE 0.016 0.001 PHE A 387 TYR 0.024 0.001 TYR B 459 ARG 0.002 0.000 ARG C 125 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 16) link_NAG-ASN : angle 1.83579 ( 48) link_BETA1-4 : bond 0.00223 ( 9) link_BETA1-4 : angle 1.24351 ( 27) hydrogen bonds : bond 0.03261 ( 414) hydrogen bonds : angle 4.96582 ( 1209) SS BOND : bond 0.00253 ( 13) SS BOND : angle 1.36854 ( 26) covalent geometry : bond 0.00380 (14193) covalent geometry : angle 0.50249 (19300) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3292 Ramachandran restraints generated. 1646 Oldfield, 0 Emsley, 1646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 65 time to evaluate : 1.474 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8508 (mp10) REVERT: A 162 HIS cc_start: 0.8786 (OUTLIER) cc_final: 0.7568 (p-80) REVERT: A 262 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8776 (m) REVERT: A 445 LEU cc_start: 0.9325 (mt) cc_final: 0.9067 (mt) REVERT: A 452 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8091 (pm20) REVERT: A 715 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8121 (mt0) REVERT: C 557 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8898 (p) REVERT: C 715 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8328 (mt0) REVERT: B 429 CYS cc_start: 0.6630 (OUTLIER) cc_final: 0.6340 (p) REVERT: B 474 LYS cc_start: 0.7856 (ttmt) cc_final: 0.7515 (tppt) REVERT: B 572 GLN cc_start: 0.6357 (OUTLIER) cc_final: 0.5814 (mm-40) outliers start: 37 outliers final: 28 residues processed: 98 average time/residue: 0.2148 time to fit residues: 34.1092 Evaluate side-chains 100 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 63 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 177 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 452 GLU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 715 GLN Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 385 CYS Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 557 THR Chi-restraints excluded: chain C residue 715 GLN Chi-restraints excluded: chain C residue 736 THR Chi-restraints excluded: chain C residue 739 ASP Chi-restraints excluded: chain B residue 429 CYS Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 493 THR Chi-restraints excluded: chain B residue 504 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 163 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 8 optimal weight: 0.0770 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.073251 restraints weight = 28375.583| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.91 r_work: 0.2842 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14231 Z= 0.132 Angle : 0.492 9.281 19401 Z= 0.254 Chirality : 0.043 0.227 2123 Planarity : 0.003 0.041 2425 Dihedral : 5.195 58.480 2364 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.56 % Allowed : 17.46 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.20), residues: 1646 helix: 0.57 (0.33), residues: 262 sheet: -0.49 (0.22), residues: 542 loop : -0.86 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 157 HIS 0.003 0.001 HIS C 483 PHE 0.016 0.001 PHE A 387 TYR 0.028 0.001 TYR B 459 ARG 0.002 0.000 ARG C 453 Details of bonding type rmsd link_NAG-ASN : bond 0.00184 ( 16) link_NAG-ASN : angle 1.76780 ( 48) link_BETA1-4 : bond 0.00260 ( 9) link_BETA1-4 : angle 1.19956 ( 27) hydrogen bonds : bond 0.03106 ( 414) hydrogen bonds : angle 4.88584 ( 1209) SS BOND : bond 0.00236 ( 13) SS BOND : angle 1.20691 ( 26) covalent geometry : bond 0.00305 (14193) covalent geometry : angle 0.48101 (19300) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6827.90 seconds wall clock time: 125 minutes 7.92 seconds (7507.92 seconds total)