Starting phenix.real_space_refine on Thu Sep 18 04:00:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmj_61604/09_2025/9jmj_61604.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmj_61604/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jmj_61604/09_2025/9jmj_61604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmj_61604/09_2025/9jmj_61604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jmj_61604/09_2025/9jmj_61604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmj_61604/09_2025/9jmj_61604.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.07, per 1000 atoms: 0.22 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: 1.16 Conformation dependent library (CDL) restraints added in 638.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.51 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: 2.35 Time building geometry restraints manager: 1.57 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: 2.930 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.310 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.070 ------------------------------------------------------------------------------- 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 : 4.67 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.19), 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 ARG 0.015 0.001 ARG B 405 TYR 0.036 0.002 TYR A 422 PHE 0.024 0.001 PHE B 533 TRP 0.028 0.001 TRP C 627 HIS 0.005 0.001 HIS C 754 Details of bonding type rmsd covalent geometry : bond 0.00368 (14193) covalent geometry : angle 0.65260 (19300) SS BOND : bond 0.00568 ( 13) SS BOND : angle 1.46046 ( 26) hydrogen bonds : bond 0.21095 ( 414) hydrogen bonds : angle 8.61465 ( 1209) link_BETA1-4 : bond 0.00660 ( 9) link_BETA1-4 : angle 1.87046 ( 27) link_NAG-ASN : bond 0.00201 ( 16) link_NAG-ASN : angle 1.73267 ( 48) *********************** 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 : 0.485 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: 0.1016 time to fit residues: 14.1753 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 : 0.516 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.094841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.077437 restraints weight = 27659.298| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 1.94 r_work: 0.2931 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14231 Z= 0.127 Angle : 0.514 9.825 19401 Z= 0.268 Chirality : 0.044 0.237 2123 Planarity : 0.004 0.042 2425 Dihedral : 7.685 67.090 2364 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.69 % Allowed : 16.39 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.92 (0.20), residues: 1646 helix: 0.28 (0.33), residues: 234 sheet: -0.16 (0.22), residues: 508 loop : -1.10 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 405 TYR 0.027 0.001 TYR B 459 PHE 0.016 0.001 PHE A 371 TRP 0.012 0.001 TRP C 627 HIS 0.004 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00281 (14193) covalent geometry : angle 0.50333 (19300) SS BOND : bond 0.00283 ( 13) SS BOND : angle 0.94261 ( 26) hydrogen bonds : bond 0.04066 ( 414) hydrogen bonds : angle 5.82583 ( 1209) link_BETA1-4 : bond 0.00300 ( 9) link_BETA1-4 : angle 1.59090 ( 27) link_NAG-ASN : bond 0.00201 ( 16) link_NAG-ASN : angle 1.68353 ( 48) *********************** 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: 25 poor density : 81 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 528 MET cc_start: 0.8513 (mtm) cc_final: 0.8182 (mtm) REVERT: C 310 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8150 (ttp-110) REVERT: C 715 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: B 429 CYS cc_start: 0.6383 (OUTLIER) cc_final: 0.5457 (p) REVERT: B 474 LYS cc_start: 0.7636 (ttmt) cc_final: 0.6888 (tppt) REVERT: B 507 SER cc_start: 0.8896 (p) cc_final: 0.8547 (t) REVERT: B 517 GLU cc_start: 0.7779 (tp30) cc_final: 0.6766 (tp30) REVERT: B 572 GLN cc_start: 0.6574 (mt0) cc_final: 0.5627 (tp40) outliers start: 25 outliers final: 10 residues processed: 103 average time/residue: 0.0952 time to fit residues: 15.3541 Evaluate side-chains 88 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 390 ASP Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 487 ASN Chi-restraints excluded: chain C residue 310 ARG Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 715 GLN 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 133 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.094220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.076832 restraints weight = 27905.186| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.95 r_work: 0.2912 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14231 Z= 0.109 Angle : 0.482 9.765 19401 Z= 0.249 Chirality : 0.043 0.232 2123 Planarity : 0.003 0.040 2425 Dihedral : 6.411 58.852 2364 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.63 % Allowed : 15.71 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.20), residues: 1646 helix: 0.79 (0.34), residues: 232 sheet: -0.20 (0.22), residues: 508 loop : -1.01 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 140 TYR 0.015 0.001 TYR C 105 PHE 0.022 0.001 PHE B 403 TRP 0.011 0.001 TRP A 629 HIS 0.003 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00244 (14193) covalent geometry : angle 0.47336 (19300) SS BOND : bond 0.00207 ( 13) SS BOND : angle 0.70259 ( 26) hydrogen bonds : bond 0.03425 ( 414) hydrogen bonds : angle 5.21843 ( 1209) link_BETA1-4 : bond 0.00340 ( 9) link_BETA1-4 : angle 1.48185 ( 27) link_NAG-ASN : bond 0.00169 ( 16) link_NAG-ASN : angle 1.56502 ( 48) *********************** 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 119 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 80 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8405 (mm-40) REVERT: C 715 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: B 429 CYS cc_start: 0.6421 (OUTLIER) cc_final: 0.5436 (p) REVERT: B 474 LYS cc_start: 0.7697 (ttmt) cc_final: 0.7001 (tppt) REVERT: B 572 GLN cc_start: 0.6487 (mt0) cc_final: 0.5497 (tp40) outliers start: 39 outliers final: 23 residues processed: 116 average time/residue: 0.1079 time to fit residues: 19.2712 Evaluate side-chains 98 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 72 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 A residue 675 THR 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 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 498 SER 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 87 optimal weight: 0.4980 chunk 12 optimal weight: 6.9990 chunk 152 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 45 optimal weight: 0.0570 chunk 88 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 overall best weight: 2.3104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 718 GLN C 314 GLN C 483 HIS C 508 GLN B 475 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.089670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.072343 restraints weight = 28397.272| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 1.95 r_work: 0.2820 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 14231 Z= 0.236 Angle : 0.580 9.239 19401 Z= 0.301 Chirality : 0.046 0.229 2123 Planarity : 0.004 0.034 2425 Dihedral : 6.209 59.948 2364 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.10 % Allowed : 16.79 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.01 (0.20), residues: 1646 helix: 0.28 (0.32), residues: 261 sheet: -0.60 (0.22), residues: 511 loop : -0.94 (0.20), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 253 TYR 0.019 0.002 TYR C 752 PHE 0.020 0.002 PHE A 387 TRP 0.019 0.002 TRP A 629 HIS 0.006 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00549 (14193) covalent geometry : angle 0.56871 (19300) SS BOND : bond 0.00446 ( 13) SS BOND : angle 0.85898 ( 26) hydrogen bonds : bond 0.03897 ( 414) hydrogen bonds : angle 5.35395 ( 1209) link_BETA1-4 : bond 0.00214 ( 9) link_BETA1-4 : angle 1.60196 ( 27) link_NAG-ASN : bond 0.00308 ( 16) link_NAG-ASN : angle 1.97725 ( 48) *********************** 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 115 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 69 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8585 (mp10) REVERT: A 715 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: C 557 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8842 (p) REVERT: C 715 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8308 (mt0) REVERT: B 429 CYS cc_start: 0.6577 (OUTLIER) cc_final: 0.5663 (p) REVERT: B 474 LYS cc_start: 0.7791 (ttmt) cc_final: 0.7470 (tppt) REVERT: B 572 GLN cc_start: 0.6352 (OUTLIER) cc_final: 0.5463 (tp40) outliers start: 46 outliers final: 30 residues processed: 107 average time/residue: 0.0893 time to fit residues: 15.5011 Evaluate side-chains 100 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 64 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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 283 THR 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 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 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 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 504 SER 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 102 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 15 optimal weight: 0.0020 chunk 75 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.7592 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.091511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.074214 restraints weight = 28102.769| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.95 r_work: 0.2860 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14231 Z= 0.105 Angle : 0.480 9.204 19401 Z= 0.248 Chirality : 0.043 0.226 2123 Planarity : 0.003 0.040 2425 Dihedral : 5.703 59.666 2364 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.76 % Allowed : 17.06 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.20), residues: 1646 helix: 0.64 (0.33), residues: 250 sheet: -0.49 (0.22), residues: 523 loop : -0.90 (0.20), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 471 TYR 0.012 0.001 TYR C 752 PHE 0.016 0.001 PHE A 387 TRP 0.012 0.001 TRP A 157 HIS 0.004 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00236 (14193) covalent geometry : angle 0.46869 (19300) SS BOND : bond 0.00351 ( 13) SS BOND : angle 1.36216 ( 26) hydrogen bonds : bond 0.03132 ( 414) hydrogen bonds : angle 5.04264 ( 1209) link_BETA1-4 : bond 0.00280 ( 9) link_BETA1-4 : angle 1.29536 ( 27) link_NAG-ASN : bond 0.00169 ( 16) link_NAG-ASN : angle 1.66029 ( 48) *********************** 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 109 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 68 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.8419 (mm-40) REVERT: A 715 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: C 557 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8766 (p) REVERT: C 715 GLN cc_start: 0.9044 (OUTLIER) cc_final: 0.8262 (mt0) REVERT: B 429 CYS cc_start: 0.6426 (OUTLIER) cc_final: 0.5492 (p) REVERT: B 460 MET cc_start: 0.7100 (ttp) cc_final: 0.6894 (ttp) REVERT: B 474 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7573 (tppt) REVERT: B 572 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.5482 (tp40) outliers start: 41 outliers final: 26 residues processed: 104 average time/residue: 0.0889 time to fit residues: 14.6524 Evaluate side-chains 97 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 202 VAL Chi-restraints excluded: chain A residue 262 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 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 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 217 SER Chi-restraints excluded: chain C residue 251 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 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 498 SER Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 572 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 110 optimal weight: 0.0270 chunk 113 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 14 optimal weight: 0.0270 chunk 147 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 overall best weight: 0.5096 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.092601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.075547 restraints weight = 27823.783| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.91 r_work: 0.2886 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1969 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= 0.086 Angle : 0.455 9.396 19401 Z= 0.236 Chirality : 0.042 0.229 2123 Planarity : 0.003 0.041 2425 Dihedral : 5.226 59.255 2364 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.70 % Allowed : 17.94 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.85 (0.20), residues: 1646 helix: 0.80 (0.34), residues: 250 sheet: -0.58 (0.22), residues: 538 loop : -0.91 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.011 0.001 TYR C 414 PHE 0.015 0.001 PHE A 387 TRP 0.012 0.001 TRP A 157 HIS 0.004 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00187 (14193) covalent geometry : angle 0.44653 (19300) SS BOND : bond 0.00204 ( 13) SS BOND : angle 0.65201 ( 26) hydrogen bonds : bond 0.02878 ( 414) hydrogen bonds : angle 4.80418 ( 1209) link_BETA1-4 : bond 0.00315 ( 9) link_BETA1-4 : angle 1.22423 ( 27) link_NAG-ASN : bond 0.00168 ( 16) link_NAG-ASN : angle 1.53708 ( 48) *********************** 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 112 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 72 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8387 (mm-40) REVERT: A 715 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7953 (mt0) REVERT: C 557 THR cc_start: 0.9064 (OUTLIER) cc_final: 0.8838 (p) REVERT: C 715 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: B 429 CYS cc_start: 0.6420 (OUTLIER) cc_final: 0.5983 (p) REVERT: B 474 LYS cc_start: 0.7838 (ttmt) cc_final: 0.7586 (ttmm) REVERT: B 572 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.5609 (tp40) outliers start: 40 outliers final: 26 residues processed: 106 average time/residue: 0.0960 time to fit residues: 16.0768 Evaluate side-chains 98 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 66 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 GLN Chi-restraints excluded: chain A residue 142 LEU 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 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 217 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 395 THR Chi-restraints excluded: chain C residue 472 CYS 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 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 75 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 142 optimal weight: 0.0050 chunk 14 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.090788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.073633 restraints weight = 28221.916| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.92 r_work: 0.2854 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14231 Z= 0.144 Angle : 0.490 9.394 19401 Z= 0.253 Chirality : 0.043 0.230 2123 Planarity : 0.003 0.039 2425 Dihedral : 5.225 59.543 2364 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.24 % Allowed : 17.40 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.20), residues: 1646 helix: 0.57 (0.33), residues: 262 sheet: -0.47 (0.22), residues: 520 loop : -0.91 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 471 TYR 0.015 0.001 TYR C 752 PHE 0.016 0.001 PHE A 387 TRP 0.008 0.001 TRP A 157 HIS 0.004 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00331 (14193) covalent geometry : angle 0.48073 (19300) SS BOND : bond 0.00251 ( 13) SS BOND : angle 0.80548 ( 26) hydrogen bonds : bond 0.03153 ( 414) hydrogen bonds : angle 4.89401 ( 1209) link_BETA1-4 : bond 0.00225 ( 9) link_BETA1-4 : angle 1.27735 ( 27) link_NAG-ASN : bond 0.00191 ( 16) link_NAG-ASN : angle 1.67892 ( 48) *********************** 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 112 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 64 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8412 (mm-40) REVERT: A 293 MET cc_start: 0.8445 (mtt) cc_final: 0.8187 (mtt) REVERT: A 638 MET cc_start: 0.8929 (mmt) cc_final: 0.8679 (mmm) REVERT: A 715 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8031 (mt0) REVERT: C 557 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8887 (p) REVERT: C 715 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8343 (mt0) REVERT: B 418 LEU cc_start: 0.7513 (pt) cc_final: 0.6424 (tt) REVERT: B 429 CYS cc_start: 0.6548 (OUTLIER) cc_final: 0.6100 (p) REVERT: B 474 LYS cc_start: 0.7871 (ttmt) cc_final: 0.7593 (ttmm) REVERT: B 572 GLN cc_start: 0.6550 (OUTLIER) cc_final: 0.5780 (tp40) outliers start: 48 outliers final: 37 residues processed: 105 average time/residue: 0.1025 time to fit residues: 17.0708 Evaluate side-chains 106 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 63 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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 142 LEU 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 675 THR Chi-restraints excluded: chain A residue 715 GLN Chi-restraints excluded: chain C residue 66 HIS 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 217 SER Chi-restraints excluded: chain C residue 251 THR 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 472 CYS Chi-restraints excluded: chain C residue 542 LEU 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 Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 86 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 83 optimal weight: 0.0170 chunk 103 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.073700 restraints weight = 27941.813| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.92 r_work: 0.2855 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14231 Z= 0.133 Angle : 0.482 9.323 19401 Z= 0.249 Chirality : 0.043 0.227 2123 Planarity : 0.003 0.040 2425 Dihedral : 5.167 59.883 2364 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.03 % Allowed : 17.40 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.20), residues: 1646 helix: 0.58 (0.33), residues: 262 sheet: -0.49 (0.22), residues: 522 loop : -0.90 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 453 TYR 0.014 0.001 TYR C 752 PHE 0.016 0.001 PHE A 387 TRP 0.010 0.001 TRP A 157 HIS 0.008 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00307 (14193) covalent geometry : angle 0.47330 (19300) SS BOND : bond 0.00233 ( 13) SS BOND : angle 0.77234 ( 26) hydrogen bonds : bond 0.03072 ( 414) hydrogen bonds : angle 4.87136 ( 1209) link_BETA1-4 : bond 0.00245 ( 9) link_BETA1-4 : angle 1.24119 ( 27) link_NAG-ASN : bond 0.00165 ( 16) link_NAG-ASN : angle 1.66242 ( 48) *********************** 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 108 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 63 time to evaluate : 0.591 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.8412 (mm-40) REVERT: A 293 MET cc_start: 0.8380 (mtt) cc_final: 0.8093 (mtt) REVERT: A 638 MET cc_start: 0.8907 (mmt) cc_final: 0.8618 (mmm) REVERT: A 715 GLN cc_start: 0.8982 (OUTLIER) cc_final: 0.8044 (mt0) REVERT: C 557 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8882 (p) REVERT: C 715 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8342 (mt0) REVERT: B 429 CYS cc_start: 0.6548 (OUTLIER) cc_final: 0.6136 (p) REVERT: B 474 LYS cc_start: 0.7894 (ttmt) cc_final: 0.7601 (tppt) REVERT: B 572 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.5839 (tp40) outliers start: 45 outliers final: 34 residues processed: 102 average time/residue: 0.1046 time to fit residues: 17.0805 Evaluate side-chains 102 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 62 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 142 LEU 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 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 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 217 SER Chi-restraints excluded: chain C residue 251 THR 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 472 CYS 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 Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.090724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.073582 restraints weight = 28209.066| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.93 r_work: 0.2846 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14231 Z= 0.132 Angle : 0.480 9.283 19401 Z= 0.249 Chirality : 0.043 0.226 2123 Planarity : 0.003 0.040 2425 Dihedral : 5.131 59.641 2364 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.83 % Allowed : 17.80 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.20), residues: 1646 helix: 0.60 (0.33), residues: 262 sheet: -0.42 (0.22), residues: 532 loop : -0.89 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 453 TYR 0.014 0.001 TYR C 752 PHE 0.016 0.001 PHE A 387 TRP 0.010 0.001 TRP A 157 HIS 0.004 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00302 (14193) covalent geometry : angle 0.47130 (19300) SS BOND : bond 0.00233 ( 13) SS BOND : angle 0.78659 ( 26) hydrogen bonds : bond 0.03054 ( 414) hydrogen bonds : angle 4.84460 ( 1209) link_BETA1-4 : bond 0.00250 ( 9) link_BETA1-4 : angle 1.21474 ( 27) link_NAG-ASN : bond 0.00170 ( 16) link_NAG-ASN : angle 1.66910 ( 48) *********************** 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 108 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 66 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8413 (mm-40) REVERT: A 237 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8017 (mt-10) REVERT: A 293 MET cc_start: 0.8404 (mtt) cc_final: 0.8124 (mtt) REVERT: A 638 MET cc_start: 0.8911 (mmt) cc_final: 0.8662 (mmm) REVERT: A 715 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: C 557 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8915 (p) REVERT: C 715 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: B 429 CYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6250 (p) REVERT: B 474 LYS cc_start: 0.7892 (ttmt) cc_final: 0.7578 (tppt) REVERT: B 572 GLN cc_start: 0.6541 (OUTLIER) cc_final: 0.5840 (tp40) outliers start: 42 outliers final: 34 residues processed: 102 average time/residue: 0.1026 time to fit residues: 16.8095 Evaluate side-chains 104 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 64 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 142 LEU 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 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 616 MET Chi-restraints excluded: chain A residue 653 VAL 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 217 SER Chi-restraints excluded: chain C residue 251 THR 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 472 CYS Chi-restraints excluded: chain C residue 542 LEU 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 Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 99 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 77 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 chunk 131 optimal weight: 3.9990 chunk 123 optimal weight: 0.0980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.091453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.074346 restraints weight = 27970.292| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.93 r_work: 0.2868 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2297 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= 0.104 Angle : 0.471 9.362 19401 Z= 0.244 Chirality : 0.043 0.227 2123 Planarity : 0.003 0.041 2425 Dihedral : 5.045 59.887 2364 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.56 % Allowed : 18.27 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.76 (0.20), residues: 1646 helix: 0.65 (0.33), residues: 262 sheet: -0.42 (0.22), residues: 534 loop : -0.87 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 253 TYR 0.025 0.001 TYR B 459 PHE 0.015 0.001 PHE A 387 TRP 0.011 0.001 TRP A 157 HIS 0.004 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00236 (14193) covalent geometry : angle 0.46318 (19300) SS BOND : bond 0.00204 ( 13) SS BOND : angle 0.71261 ( 26) hydrogen bonds : bond 0.02942 ( 414) hydrogen bonds : angle 4.76973 ( 1209) link_BETA1-4 : bond 0.00312 ( 9) link_BETA1-4 : angle 1.16348 ( 27) link_NAG-ASN : bond 0.00157 ( 16) link_NAG-ASN : angle 1.59624 ( 48) ********************** 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 103 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 65 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 112 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8396 (mm-40) REVERT: A 237 GLU cc_start: 0.8229 (mt-10) cc_final: 0.8021 (mt-10) REVERT: A 293 MET cc_start: 0.8335 (mtt) cc_final: 0.8071 (mtt) REVERT: A 715 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8014 (mt0) REVERT: C 557 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8899 (p) REVERT: C 715 GLN cc_start: 0.9076 (OUTLIER) cc_final: 0.8330 (mt0) REVERT: B 429 CYS cc_start: 0.6560 (OUTLIER) cc_final: 0.6326 (p) REVERT: B 460 MET cc_start: 0.7152 (ttp) cc_final: 0.6833 (ttp) REVERT: B 474 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7578 (tppt) REVERT: B 572 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.5855 (tp40) outliers start: 38 outliers final: 32 residues processed: 99 average time/residue: 0.1030 time to fit residues: 16.3886 Evaluate side-chains 102 residues out of total 1483 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 64 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 142 LEU 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 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 616 MET Chi-restraints excluded: chain A residue 653 VAL 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 217 SER Chi-restraints excluded: chain C residue 251 THR 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 472 CYS 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 Chi-restraints excluded: chain B residue 577 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.091570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.074535 restraints weight = 28057.443| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 1.90 r_work: 0.2874 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14231 Z= 0.104 Angle : 0.465 9.351 19401 Z= 0.240 Chirality : 0.043 0.228 2123 Planarity : 0.003 0.041 2425 Dihedral : 4.956 59.956 2364 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.49 % Allowed : 18.48 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.20), residues: 1646 helix: 0.69 (0.33), residues: 262 sheet: -0.43 (0.22), residues: 542 loop : -0.84 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 253 TYR 0.026 0.001 TYR B 459 PHE 0.016 0.001 PHE A 387 TRP 0.011 0.001 TRP A 157 HIS 0.004 0.001 HIS C 483 Details of bonding type rmsd covalent geometry : bond 0.00236 (14193) covalent geometry : angle 0.45651 (19300) SS BOND : bond 0.00200 ( 13) SS BOND : angle 0.71619 ( 26) hydrogen bonds : bond 0.02887 ( 414) hydrogen bonds : angle 4.70926 ( 1209) link_BETA1-4 : bond 0.00279 ( 9) link_BETA1-4 : angle 1.14887 ( 27) link_NAG-ASN : bond 0.00158 ( 16) link_NAG-ASN : angle 1.57756 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2821.96 seconds wall clock time: 49 minutes 26.57 seconds (2966.57 seconds total)