Starting phenix.real_space_refine on Thu Jul 31 17:04:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmm_61606/07_2025/9jmm_61606.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmm_61606/07_2025/9jmm_61606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jmm_61606/07_2025/9jmm_61606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmm_61606/07_2025/9jmm_61606.map" model { file = "/net/cci-nas-00/data/ceres_data/9jmm_61606/07_2025/9jmm_61606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmm_61606/07_2025/9jmm_61606.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.152 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 63 5.16 5 C 8806 2.51 5 N 2226 2.21 5 O 2666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13761 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: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1466 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 12, 'TRANS': 176} Chain breaks: 1 Chain: "D" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 8.09, per 1000 atoms: 0.59 Number of scatterers: 13761 At special positions: 0 Unit cell: (133.76, 147.84, 88.88, 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 63 16.00 O 2666 8.00 N 2226 7.00 C 8806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, 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=2.03 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=2.02 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 433 " - pdb=" SG CYS B 486 " distance=2.04 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS B 534 " 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 ALPHA1-2 " MAN D 4 " - " MAN D 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " 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 A 801 " - " ASN A 92 " " NAG A 802 " - " ASN A 85 " " NAG A 803 " - " ASN A 150 " " NAG A 804 " - " ASN A 685 " " NAG C 801 " - " ASN C 92 " " NAG C 802 " - " ASN C 85 " " NAG C 803 " - " ASN C 685 " " NAG C 804 " - " ASN C 150 " " NAG D 1 " - " ASN A 229 " " NAG E 1 " - " ASN A 321 " " NAG F 1 " - " ASN A 219 " " NAG G 1 " - " ASN A 281 " " NAG H 1 " - " ASN C 219 " " NAG I 1 " - " ASN C 229 " " NAG J 1 " - " ASN C 281 " " NAG K 1 " - " ASN C 321 " Time building additional restraints: 3.26 Conformation dependent library (CDL) restraints added in 1.6 seconds 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3098 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 26 sheets defined 21.0% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 91 through 97 removed outlier: 4.418A pdb=" N PHE A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 91 through 97' Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 274 through 276 No H-bonds generated for 'chain 'A' and resid 274 through 276' Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.519A pdb=" N ILE A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 Processing helix chain 'A' and resid 421 through 425 Processing helix chain 'A' and resid 497 through 504 Processing helix chain 'A' and resid 562 through 570 removed outlier: 3.633A pdb=" N TYR A 566 " --> pdb=" O ASN A 562 " (cutoff:3.500A) 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 600 through 617 removed outlier: 4.163A pdb=" N GLY A 617 " --> pdb=" O PHE A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 641 Processing helix chain 'A' and resid 663 through 671 removed outlier: 3.688A 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: 4.950A pdb=" N GLU A 693 " --> pdb=" O SER A 690 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 696 " --> pdb=" O GLU A 693 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN A 697 " --> pdb=" O ASN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 727 removed outlier: 4.282A 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: 3.719A pdb=" N PHE C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE C 98 " --> pdb=" O THR C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 274 through 276 No H-bonds generated for 'chain 'C' and resid 274 through 276' Processing helix chain 'C' and resid 290 through 295 removed outlier: 3.795A pdb=" N ILE C 295 " --> pdb=" O ALA C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 425 Processing helix chain 'C' and resid 497 through 505 Processing helix chain 'C' and resid 562 through 570 removed outlier: 3.641A pdb=" N TYR C 566 " --> pdb=" O ASN C 562 " (cutoff:3.500A) Processing helix chain 'C' and resid 587 through 592 removed outlier: 3.517A pdb=" N MET C 591 " --> pdb=" O GLY C 587 " (cutoff:3.500A) 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: 4.083A 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 671 removed outlier: 3.761A 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: 4.973A pdb=" N GLU C 693 " --> pdb=" O SER C 690 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS C 696 " --> pdb=" O GLU C 693 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN C 697 " --> pdb=" O ASN C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 727 Processing helix chain 'C' and resid 745 through 763 Processing helix chain 'B' and resid 393 through 398 removed outlier: 3.893A pdb=" N LEU B 397 " --> pdb=" O PHE B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 Processing helix chain 'B' and resid 442 through 446 removed outlier: 3.822A pdb=" N TYR B 446 " --> pdb=" O ARG B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 476 Processing helix chain 'B' and resid 532 through 537 removed outlier: 4.232A pdb=" N SER B 536 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 7.339A pdb=" N LYS A 41 " --> pdb=" O GLN A 508 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.531A pdb=" N GLN A 72 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE A 76 " --> pdb=" O PHE A 89 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 107 removed outlier: 3.523A pdb=" N ASP A 104 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR A 120 " --> pdb=" O THR A 129 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR A 129 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 154 through 157 removed outlier: 3.580A pdb=" N TRP A 154 " --> pdb=" O VAL A 167 " (cutoff:3.500A) 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 194 through 196 removed outlier: 4.215A pdb=" N PHE A 268 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 235 through 240 Processing sheet with id=AA8, first strand: chain 'A' and resid 298 through 307 removed outlier: 6.389A pdb=" N GLN A 314 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 303 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER A 312 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TRP A 305 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ARG A 310 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR A 322 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 298 through 307 removed outlier: 6.389A pdb=" N GLN A 314 " --> pdb=" O CYS A 301 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL A 303 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N SER A 312 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TRP A 305 " --> pdb=" O ARG A 310 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ARG A 310 " --> pdb=" O TRP A 305 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR A 322 " --> pdb=" O ARG A 317 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 363 through 364 removed outlier: 4.980A pdb=" N GLN A 388 " --> pdb=" O ASP A 393 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASP A 393 " --> pdb=" O GLN A 388 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 404 through 411 removed outlier: 5.832A pdb=" N ILE A 407 " --> pdb=" O ILE A 418 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 418 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N TYR A 414 " --> pdb=" O THR A 411 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 457 through 461 removed outlier: 7.009A pdb=" N TYR A 480 " --> pdb=" O VAL A 493 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N VAL A 493 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 482 " --> pdb=" O LEU A 491 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 511 through 518 removed outlier: 4.616A pdb=" N PHE A 578 " --> pdb=" O ASP A 545 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N TYR A 540 " --> pdb=" O ASN A 621 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ARG A 623 " --> pdb=" O TYR A 540 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TRP A 629 " --> pdb=" O VAL A 546 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N CYS A 649 " --> pdb=" O LYS A 622 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ILE A 624 " --> pdb=" O CYS A 649 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N ILE A 651 " --> pdb=" O ILE A 624 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ILE A 626 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL A 653 " --> pdb=" O ILE A 626 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLY A 628 " --> pdb=" O VAL A 653 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 67 through 72 removed outlier: 3.587A pdb=" N ASN C 80 " --> pdb=" O ASN C 85 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ASN C 85 " --> pdb=" O ASN C 80 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 104 through 107 removed outlier: 4.411A pdb=" N TYR C 120 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR C 129 " --> pdb=" O TYR C 120 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLN C 141 " --> pdb=" O ASP C 136 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.600A pdb=" N TRP C 154 " --> pdb=" O VAL C 167 " (cutoff:3.500A) 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 194 through 196 removed outlier: 4.204A pdb=" N PHE C 268 " --> pdb=" O ILE C 287 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 235 through 240 Processing sheet with id=AC2, first strand: chain 'C' and resid 298 through 307 removed outlier: 5.154A pdb=" N LEU C 300 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 316 " --> pdb=" O LEU C 300 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 302 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG C 310 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N TYR C 322 " --> pdb=" O ARG C 317 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 327 " --> pdb=" O ARG C 343 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ARG C 343 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 11.655A pdb=" N ASP C 329 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 10.938A pdb=" N VAL C 341 " --> pdb=" O ASP C 329 " (cutoff:3.500A) removed outlier: 11.241A pdb=" N ASP C 331 " --> pdb=" O CYS C 339 " (cutoff:3.500A) removed outlier: 10.629A pdb=" N CYS C 339 " --> pdb=" O ASP C 331 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 363 through 364 Processing sheet with id=AC4, first strand: chain 'C' and resid 404 through 410 removed outlier: 6.547A pdb=" N ILE C 418 " --> pdb=" O ILE C 405 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ILE C 407 " --> pdb=" O TYR C 416 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR C 416 " --> pdb=" O ILE C 407 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ALA C 409 " --> pdb=" O TYR C 414 " (cutoff:3.500A) removed outlier: 6.936A 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: 6.669A pdb=" N LEU C 482 " --> pdb=" O VAL C 493 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL C 493 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N SER C 484 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 7.404A 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: 3.572A pdb=" N VAL C 575 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N PHE C 578 " --> pdb=" O ASP C 545 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N TYR C 540 " --> pdb=" O ASP C 620 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LYS C 622 " --> pdb=" O TYR C 540 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N LEU C 542 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ILE C 624 " --> pdb=" O LEU C 542 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU C 544 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE C 626 " --> pdb=" O LEU C 544 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N VAL C 546 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY C 628 " --> pdb=" O VAL C 546 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N CYS C 649 " --> pdb=" O LYS C 622 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILE C 624 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 8.980A pdb=" N ILE C 651 " --> pdb=" O ILE C 624 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE C 626 " --> pdb=" O ILE C 651 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N VAL C 653 " --> pdb=" O ILE C 626 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLY C 628 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TYR C 700 " --> pdb=" O GLN C 731 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N MET C 733 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU C 702 " --> pdb=" O MET C 733 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N TYR C 735 " --> pdb=" O LEU C 702 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N HIS C 704 " --> pdb=" O TYR C 735 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 408 through 412 Processing sheet with id=AC8, first strand: chain 'B' and resid 521 through 523 removed outlier: 6.569A pdb=" N VAL B 565 " --> pdb=" O GLN B 508 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS B 510 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N VAL B 563 " --> pdb=" O CYS B 510 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ARG B 512 " --> pdb=" O ILE B 561 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE B 561 " --> pdb=" O ARG B 512 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU B 547 " --> pdb=" O GLY B 566 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.38 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2203 1.30 - 1.43: 4205 1.43 - 1.56: 7633 1.56 - 1.69: 4 1.69 - 1.82: 96 Bond restraints: 14141 Sorted by residual: bond pdb=" CA LEU C 567 " pdb=" C LEU C 567 " ideal model delta sigma weight residual 1.523 1.440 0.083 1.35e-02 5.49e+03 3.78e+01 bond pdb=" CA TYR A 330 " pdb=" C TYR A 330 " ideal model delta sigma weight residual 1.523 1.448 0.075 1.23e-02 6.61e+03 3.72e+01 bond pdb=" CA ARG C 358 " pdb=" C ARG C 358 " ideal model delta sigma weight residual 1.518 1.460 0.057 9.60e-03 1.09e+04 3.57e+01 bond pdb=" CA GLU C 232 " pdb=" C GLU C 232 " ideal model delta sigma weight residual 1.523 1.449 0.074 1.34e-02 5.57e+03 3.05e+01 bond pdb=" CA ALA C 564 " pdb=" CB ALA C 564 " ideal model delta sigma weight residual 1.528 1.437 0.091 1.66e-02 3.63e+03 3.01e+01 ... (remaining 14136 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 18669 2.50 - 4.99: 473 4.99 - 7.49: 61 7.49 - 9.99: 20 9.99 - 12.49: 2 Bond angle restraints: 19225 Sorted by residual: angle pdb=" N VAL C 266 " pdb=" CA VAL C 266 " pdb=" C VAL C 266 " ideal model delta sigma weight residual 108.48 120.97 -12.49 1.44e+00 4.82e-01 7.52e+01 angle pdb=" N LYS C 392 " pdb=" CA LYS C 392 " pdb=" C LYS C 392 " ideal model delta sigma weight residual 111.28 120.00 -8.72 1.09e+00 8.42e-01 6.40e+01 angle pdb=" N PHE C 357 " pdb=" CA PHE C 357 " pdb=" C PHE C 357 " ideal model delta sigma weight residual 114.56 105.02 9.54 1.27e+00 6.20e-01 5.64e+01 angle pdb=" N GLY A 727 " pdb=" CA GLY A 727 " pdb=" C GLY A 727 " ideal model delta sigma weight residual 115.43 125.41 -9.98 1.41e+00 5.03e-01 5.01e+01 angle pdb=" N ARG C 147 " pdb=" CA ARG C 147 " pdb=" C ARG C 147 " ideal model delta sigma weight residual 110.43 119.59 -9.16 1.31e+00 5.83e-01 4.89e+01 ... (remaining 19220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 7827 21.64 - 43.28: 647 43.28 - 64.92: 136 64.92 - 86.56: 25 86.56 - 108.20: 4 Dihedral angle restraints: 8639 sinusoidal: 3775 harmonic: 4864 Sorted by residual: dihedral pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " pdb=" SG CYS C 762 " pdb=" CB CYS C 762 " ideal model delta sinusoidal sigma weight residual 93.00 161.64 -68.64 1 1.00e+01 1.00e-02 6.10e+01 dihedral pdb=" CA VAL C 546 " pdb=" C VAL C 546 " pdb=" N TYR C 547 " pdb=" CA TYR C 547 " ideal model delta harmonic sigma weight residual 180.00 155.94 24.06 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CB CYS A 649 " pdb=" SG CYS A 649 " pdb=" SG CYS A 762 " pdb=" CB CYS A 762 " ideal model delta sinusoidal sigma weight residual -86.00 -123.02 37.02 1 1.00e+01 1.00e-02 1.93e+01 ... (remaining 8636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1898 0.097 - 0.195: 196 0.195 - 0.292: 18 0.292 - 0.389: 2 0.389 - 0.487: 1 Chirality restraints: 2115 Sorted by residual: chirality pdb=" C1 NAG A 804 " pdb=" ND2 ASN A 685 " pdb=" C2 NAG A 804 " pdb=" O5 NAG A 804 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.92e+00 chirality pdb=" CA TYR A 241 " pdb=" N TYR A 241 " pdb=" C TYR A 241 " pdb=" CB TYR A 241 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA ARG C 581 " pdb=" N ARG C 581 " pdb=" C ARG C 581 " pdb=" CB ARG C 581 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2112 not shown) Planarity restraints: 2427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 687 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" C THR A 687 " 0.053 2.00e-02 2.50e+03 pdb=" O THR A 687 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL A 688 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 95 " -0.015 2.00e-02 2.50e+03 2.89e-02 8.33e+00 pdb=" C PHE C 95 " 0.050 2.00e-02 2.50e+03 pdb=" O PHE C 95 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP C 96 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 465 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO B 466 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 466 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 466 " -0.037 5.00e-02 4.00e+02 ... (remaining 2424 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 395 2.69 - 3.24: 12256 3.24 - 3.79: 21799 3.79 - 4.35: 31683 4.35 - 4.90: 51035 Nonbonded interactions: 117168 Sorted by model distance: nonbonded pdb=" OG SER B 538 " pdb=" O GLY B 541 " model vdw 2.132 3.040 nonbonded pdb=" O GLN C 508 " pdb=" OG SER C 569 " model vdw 2.237 3.040 nonbonded pdb=" O SER A 242 " pdb=" NZ LYS C 721 " model vdw 2.267 3.120 nonbonded pdb=" OG1 THR A 251 " pdb=" OE1 GLU C 237 " model vdw 2.279 3.040 nonbonded pdb=" O GLY A 672 " pdb=" OH TYR A 683 " model vdw 2.314 3.040 ... (remaining 117163 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 'E' 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 33.550 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 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 : 0.008 0.091 14180 Z= 0.580 Angle : 0.913 12.486 19330 Z= 0.572 Chirality : 0.059 0.487 2115 Planarity : 0.005 0.067 2411 Dihedral : 16.108 108.203 5505 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.02 % Allowed : 19.55 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1637 helix: -0.15 (0.32), residues: 258 sheet: 0.36 (0.22), residues: 535 loop : -0.93 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 201 HIS 0.011 0.001 HIS A 704 PHE 0.025 0.001 PHE C 461 TYR 0.030 0.002 TYR C 468 ARG 0.006 0.001 ARG A 310 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 16) link_NAG-ASN : angle 2.31034 ( 48) link_BETA1-4 : bond 0.00303 ( 9) link_BETA1-4 : angle 1.50830 ( 27) link_ALPHA1-2 : bond 0.00613 ( 1) link_ALPHA1-2 : angle 1.50658 ( 3) link_ALPHA1-3 : bond 0.00363 ( 1) link_ALPHA1-3 : angle 1.62168 ( 3) hydrogen bonds : bond 0.20224 ( 451) hydrogen bonds : angle 7.31298 ( 1242) SS BOND : bond 0.00533 ( 12) SS BOND : angle 1.69724 ( 24) covalent geometry : bond 0.00840 (14141) covalent geometry : angle 0.90404 (19225) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 1.517 Fit side-chains revert: symmetry clash REVERT: A 392 LYS cc_start: 0.7905 (mmtt) cc_final: 0.7432 (mmpt) REVERT: A 538 LYS cc_start: 0.8181 (mtpm) cc_final: 0.7916 (mttp) REVERT: C 391 LYS cc_start: 0.7898 (ttmt) cc_final: 0.7426 (mmtm) REVERT: B 427 MET cc_start: 0.6602 (OUTLIER) cc_final: 0.6150 (ptt) outliers start: 15 outliers final: 7 residues processed: 179 average time/residue: 1.2469 time to fit residues: 244.7581 Evaluate side-chains 167 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 394 CYS Chi-restraints excluded: chain C residue 472 CYS Chi-restraints excluded: chain B residue 427 MET Chi-restraints excluded: chain B residue 582 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9990 chunk 122 optimal weight: 0.0060 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 65 optimal weight: 0.0270 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 94 optimal weight: 0.9980 chunk 147 optimal weight: 20.0000 overall best weight: 0.8058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 138 ASN A 141 GLN A 553 GLN A 621 ASN A 704 HIS C 314 GLN C 383 HIS C 761 GLN B 476 ASN B 483 ASN B 584 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.127635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.097213 restraints weight = 14747.891| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.63 r_work: 0.2828 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14180 Z= 0.111 Angle : 0.539 11.870 19330 Z= 0.285 Chirality : 0.044 0.396 2115 Planarity : 0.004 0.061 2411 Dihedral : 7.732 75.955 2407 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.18 % Allowed : 18.32 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.20), residues: 1637 helix: -0.02 (0.33), residues: 248 sheet: 0.29 (0.22), residues: 535 loop : -0.76 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 157 HIS 0.004 0.001 HIS C 748 PHE 0.019 0.001 PHE A 387 TYR 0.016 0.001 TYR C 752 ARG 0.003 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 16) link_NAG-ASN : angle 1.79974 ( 48) link_BETA1-4 : bond 0.00418 ( 9) link_BETA1-4 : angle 1.37527 ( 27) link_ALPHA1-2 : bond 0.00852 ( 1) link_ALPHA1-2 : angle 1.77467 ( 3) link_ALPHA1-3 : bond 0.01343 ( 1) link_ALPHA1-3 : angle 1.94335 ( 3) hydrogen bonds : bond 0.04241 ( 451) hydrogen bonds : angle 5.39958 ( 1242) SS BOND : bond 0.00179 ( 12) SS BOND : angle 1.10344 ( 24) covalent geometry : bond 0.00238 (14141) covalent geometry : angle 0.52841 (19225) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 1.511 Fit side-chains REVERT: A 76 ILE cc_start: 0.8095 (OUTLIER) cc_final: 0.7882 (mm) REVERT: A 489 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8421 (tttm) REVERT: A 538 LYS cc_start: 0.8073 (mtpm) cc_final: 0.7789 (mttp) REVERT: A 589 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8194 (tttm) REVERT: C 71 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8502 (tttm) REVERT: C 191 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8040 (tm-30) outliers start: 32 outliers final: 10 residues processed: 186 average time/residue: 1.2147 time to fit residues: 249.9400 Evaluate side-chains 168 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 153 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 472 CYS Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 141 GLN A 505 GLN A 553 GLN A 621 ASN C 51 ASN C 505 GLN C 761 GLN B 406 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 479 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.124837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.094062 restraints weight = 14923.233| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.60 r_work: 0.2751 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14180 Z= 0.177 Angle : 0.587 10.874 19330 Z= 0.306 Chirality : 0.047 0.523 2115 Planarity : 0.004 0.061 2411 Dihedral : 6.840 60.336 2397 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.66 % Allowed : 17.57 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1637 helix: -0.05 (0.33), residues: 248 sheet: 0.21 (0.21), residues: 535 loop : -0.79 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 201 HIS 0.004 0.001 HIS C 748 PHE 0.022 0.001 PHE C 387 TYR 0.017 0.002 TYR A 752 ARG 0.003 0.000 ARG B 535 Details of bonding type rmsd link_NAG-ASN : bond 0.00150 ( 16) link_NAG-ASN : angle 2.15840 ( 48) link_BETA1-4 : bond 0.00306 ( 9) link_BETA1-4 : angle 1.55926 ( 27) link_ALPHA1-2 : bond 0.00870 ( 1) link_ALPHA1-2 : angle 1.79599 ( 3) link_ALPHA1-3 : bond 0.01170 ( 1) link_ALPHA1-3 : angle 1.66764 ( 3) hydrogen bonds : bond 0.04473 ( 451) hydrogen bonds : angle 5.20650 ( 1242) SS BOND : bond 0.00120 ( 12) SS BOND : angle 1.82170 ( 24) covalent geometry : bond 0.00423 (14141) covalent geometry : angle 0.57149 (19225) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 1.394 Fit side-chains REVERT: A 538 LYS cc_start: 0.8201 (mtpm) cc_final: 0.7881 (mttp) REVERT: A 589 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8187 (tttm) REVERT: A 591 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8551 (ttt) REVERT: A 621 ASN cc_start: 0.7832 (m110) cc_final: 0.7594 (m-40) REVERT: C 71 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8483 (tttm) outliers start: 39 outliers final: 13 residues processed: 180 average time/residue: 1.2369 time to fit residues: 244.4149 Evaluate side-chains 170 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 471 ARG Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain B residue 450 THR Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 94 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 10 optimal weight: 0.0980 chunk 20 optimal weight: 0.4980 chunk 141 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 112 optimal weight: 8.9990 chunk 68 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 147 optimal weight: 30.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 141 GLN A 298 HIS C 51 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 505 GLN C 761 GLN B 406 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.094667 restraints weight = 14845.540| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.61 r_work: 0.2791 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14180 Z= 0.134 Angle : 0.542 11.128 19330 Z= 0.282 Chirality : 0.045 0.410 2115 Planarity : 0.004 0.060 2411 Dihedral : 5.998 54.226 2396 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.72 % Allowed : 17.85 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1637 helix: 0.08 (0.33), residues: 246 sheet: 0.17 (0.21), residues: 535 loop : -0.80 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 157 HIS 0.004 0.001 HIS C 748 PHE 0.020 0.001 PHE A 387 TYR 0.017 0.001 TYR C 752 ARG 0.002 0.000 ARG B 535 Details of bonding type rmsd link_NAG-ASN : bond 0.00204 ( 16) link_NAG-ASN : angle 1.95973 ( 48) link_BETA1-4 : bond 0.00284 ( 9) link_BETA1-4 : angle 1.55039 ( 27) link_ALPHA1-2 : bond 0.00922 ( 1) link_ALPHA1-2 : angle 1.63356 ( 3) link_ALPHA1-3 : bond 0.01069 ( 1) link_ALPHA1-3 : angle 1.66490 ( 3) hydrogen bonds : bond 0.03815 ( 451) hydrogen bonds : angle 5.04952 ( 1242) SS BOND : bond 0.00104 ( 12) SS BOND : angle 1.73721 ( 24) covalent geometry : bond 0.00313 (14141) covalent geometry : angle 0.52757 (19225) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 147 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8074 (mtm-85) REVERT: A 538 LYS cc_start: 0.8236 (mtpm) cc_final: 0.7930 (mttp) REVERT: A 589 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8191 (tttm) REVERT: A 621 ASN cc_start: 0.7838 (m110) cc_final: 0.7616 (m-40) REVERT: C 83 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7229 (p90) REVERT: C 336 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7959 (mtp-110) REVERT: C 391 LYS cc_start: 0.7703 (ttmm) cc_final: 0.7038 (tttm) outliers start: 40 outliers final: 14 residues processed: 182 average time/residue: 1.2243 time to fit residues: 244.9328 Evaluate side-chains 170 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 489 LYS Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 0.3980 chunk 97 optimal weight: 0.0870 chunk 89 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 109 optimal weight: 0.0670 overall best weight: 1.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 141 GLN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 505 GLN C 508 GLN C 533 HIS C 761 GLN B 406 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.125177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.094022 restraints weight = 14908.853| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.63 r_work: 0.2728 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2603 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14180 Z= 0.147 Angle : 0.556 10.646 19330 Z= 0.288 Chirality : 0.046 0.522 2115 Planarity : 0.004 0.060 2411 Dihedral : 5.683 54.672 2395 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.45 % Allowed : 18.26 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1637 helix: 0.08 (0.33), residues: 246 sheet: 0.14 (0.21), residues: 535 loop : -0.80 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 157 HIS 0.005 0.001 HIS C 748 PHE 0.020 0.001 PHE A 387 TYR 0.017 0.001 TYR C 752 ARG 0.004 0.000 ARG A 471 Details of bonding type rmsd link_NAG-ASN : bond 0.00155 ( 16) link_NAG-ASN : angle 2.21194 ( 48) link_BETA1-4 : bond 0.00284 ( 9) link_BETA1-4 : angle 1.60884 ( 27) link_ALPHA1-2 : bond 0.00898 ( 1) link_ALPHA1-2 : angle 1.64793 ( 3) link_ALPHA1-3 : bond 0.01038 ( 1) link_ALPHA1-3 : angle 1.65670 ( 3) hydrogen bonds : bond 0.03881 ( 451) hydrogen bonds : angle 5.04423 ( 1242) SS BOND : bond 0.00235 ( 12) SS BOND : angle 1.80826 ( 24) covalent geometry : bond 0.00348 (14141) covalent geometry : angle 0.53853 (19225) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.621 Fit side-chains REVERT: A 51 ASN cc_start: 0.8483 (t0) cc_final: 0.8025 (t0) REVERT: A 100 HIS cc_start: 0.7279 (OUTLIER) cc_final: 0.6832 (p-80) REVERT: A 147 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8074 (mtm-85) REVERT: A 538 LYS cc_start: 0.8234 (mtpm) cc_final: 0.7903 (mttp) REVERT: A 589 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8199 (tttm) REVERT: A 616 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8261 (mtt) REVERT: A 621 ASN cc_start: 0.7843 (m110) cc_final: 0.7602 (m-40) REVERT: A 660 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: C 71 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8501 (tttm) REVERT: C 83 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7109 (p90) REVERT: C 336 ARG cc_start: 0.8184 (mtp-110) cc_final: 0.7945 (mtp-110) REVERT: C 391 LYS cc_start: 0.7668 (ttmm) cc_final: 0.7149 (ttpt) REVERT: C 536 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7724 (mmtt) REVERT: C 615 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7707 (pttt) outliers start: 36 outliers final: 14 residues processed: 179 average time/residue: 1.2879 time to fit residues: 252.4616 Evaluate side-chains 174 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 518 ILE Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 17 optimal weight: 4.9990 chunk 137 optimal weight: 0.1980 chunk 102 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 94 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 141 GLN C 51 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 533 HIS C 761 GLN B 406 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.092567 restraints weight = 15062.015| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 1.63 r_work: 0.2770 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14180 Z= 0.179 Angle : 0.582 10.551 19330 Z= 0.302 Chirality : 0.046 0.489 2115 Planarity : 0.004 0.060 2411 Dihedral : 5.539 55.742 2395 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.13 % Allowed : 17.30 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1637 helix: 0.00 (0.33), residues: 246 sheet: 0.15 (0.21), residues: 533 loop : -0.82 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 157 HIS 0.005 0.001 HIS C 682 PHE 0.020 0.001 PHE C 387 TYR 0.018 0.002 TYR C 752 ARG 0.003 0.000 ARG A 471 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 16) link_NAG-ASN : angle 2.23796 ( 48) link_BETA1-4 : bond 0.00294 ( 9) link_BETA1-4 : angle 1.68059 ( 27) link_ALPHA1-2 : bond 0.00899 ( 1) link_ALPHA1-2 : angle 1.69865 ( 3) link_ALPHA1-3 : bond 0.00926 ( 1) link_ALPHA1-3 : angle 1.74231 ( 3) hydrogen bonds : bond 0.04115 ( 451) hydrogen bonds : angle 5.07932 ( 1242) SS BOND : bond 0.00173 ( 12) SS BOND : angle 1.84898 ( 24) covalent geometry : bond 0.00428 (14141) covalent geometry : angle 0.56506 (19225) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 1.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8611 (t0) cc_final: 0.8153 (t0) REVERT: A 147 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8079 (mtm-85) REVERT: A 538 LYS cc_start: 0.8258 (mtpm) cc_final: 0.7916 (mttp) REVERT: A 660 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7626 (mp0) REVERT: C 71 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8534 (tttm) REVERT: C 83 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.7155 (p90) REVERT: C 336 ARG cc_start: 0.8208 (mtp-110) cc_final: 0.7967 (mtp-110) REVERT: C 391 LYS cc_start: 0.7766 (ttmm) cc_final: 0.7271 (ttpt) REVERT: C 503 MET cc_start: 0.8808 (mtp) cc_final: 0.8519 (mtp) REVERT: C 536 LYS cc_start: 0.8266 (mtmm) cc_final: 0.7775 (mmtt) REVERT: C 615 LYS cc_start: 0.8087 (ttpt) cc_final: 0.7737 (pttt) REVERT: B 509 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8404 (ptpt) outliers start: 46 outliers final: 17 residues processed: 189 average time/residue: 1.2341 time to fit residues: 255.9932 Evaluate side-chains 177 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 376 SER Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 35 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 123 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 141 GLN A 505 GLN A 506 ASN A 621 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 505 GLN C 533 HIS C 761 GLN B 406 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.125539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.093962 restraints weight = 14970.663| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.60 r_work: 0.2791 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2666 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14180 Z= 0.117 Angle : 0.528 10.806 19330 Z= 0.275 Chirality : 0.044 0.428 2115 Planarity : 0.004 0.060 2411 Dihedral : 5.048 57.029 2395 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.45 % Allowed : 18.19 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.20), residues: 1637 helix: 0.41 (0.34), residues: 234 sheet: 0.19 (0.21), residues: 533 loop : -0.77 (0.21), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 157 HIS 0.004 0.001 HIS C 748 PHE 0.020 0.001 PHE A 387 TYR 0.017 0.001 TYR C 752 ARG 0.003 0.000 ARG A 471 Details of bonding type rmsd link_NAG-ASN : bond 0.00199 ( 16) link_NAG-ASN : angle 1.98582 ( 48) link_BETA1-4 : bond 0.00300 ( 9) link_BETA1-4 : angle 1.55020 ( 27) link_ALPHA1-2 : bond 0.00963 ( 1) link_ALPHA1-2 : angle 1.53839 ( 3) link_ALPHA1-3 : bond 0.00926 ( 1) link_ALPHA1-3 : angle 1.48241 ( 3) hydrogen bonds : bond 0.03527 ( 451) hydrogen bonds : angle 4.94474 ( 1242) SS BOND : bond 0.00189 ( 12) SS BOND : angle 1.97165 ( 24) covalent geometry : bond 0.00271 (14141) covalent geometry : angle 0.51166 (19225) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 1.436 Fit side-chains REVERT: A 51 ASN cc_start: 0.8561 (t0) cc_final: 0.8182 (t0) REVERT: A 91 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6895 (mp0) REVERT: A 100 HIS cc_start: 0.7414 (OUTLIER) cc_final: 0.7077 (p-80) REVERT: A 147 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8062 (mtm-85) REVERT: A 538 LYS cc_start: 0.8313 (mtpm) cc_final: 0.7974 (mttp) REVERT: A 591 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.7933 (tpp) REVERT: A 616 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8191 (mtt) REVERT: A 660 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: C 83 TYR cc_start: 0.8128 (OUTLIER) cc_final: 0.7157 (p90) REVERT: C 336 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7943 (mtp-110) REVERT: C 391 LYS cc_start: 0.7660 (ttmm) cc_final: 0.7141 (ttpt) REVERT: C 503 MET cc_start: 0.8824 (mtp) cc_final: 0.8523 (mtp) REVERT: C 536 LYS cc_start: 0.8263 (mtmm) cc_final: 0.7772 (mmtt) REVERT: C 615 LYS cc_start: 0.8077 (ttpt) cc_final: 0.7748 (pttt) REVERT: B 509 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8315 (ptpt) outliers start: 36 outliers final: 14 residues processed: 177 average time/residue: 1.2716 time to fit residues: 246.2949 Evaluate side-chains 178 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 97 optimal weight: 0.3980 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 157 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 138 ASN A 141 GLN A 506 ASN A 621 ASN C 51 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN C 533 HIS C 761 GLN B 406 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.122879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.091610 restraints weight = 14957.262| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 1.64 r_work: 0.2720 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14180 Z= 0.216 Angle : 0.612 9.919 19330 Z= 0.317 Chirality : 0.047 0.422 2115 Planarity : 0.004 0.059 2411 Dihedral : 5.342 59.636 2395 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.45 % Allowed : 18.19 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.20), residues: 1637 helix: 0.24 (0.34), residues: 232 sheet: 0.16 (0.21), residues: 533 loop : -0.81 (0.20), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 201 HIS 0.005 0.001 HIS C 682 PHE 0.021 0.002 PHE A 387 TYR 0.018 0.002 TYR C 752 ARG 0.003 0.000 ARG A 471 Details of bonding type rmsd link_NAG-ASN : bond 0.00268 ( 16) link_NAG-ASN : angle 2.17174 ( 48) link_BETA1-4 : bond 0.00265 ( 9) link_BETA1-4 : angle 1.69865 ( 27) link_ALPHA1-2 : bond 0.00881 ( 1) link_ALPHA1-2 : angle 1.77391 ( 3) link_ALPHA1-3 : bond 0.00766 ( 1) link_ALPHA1-3 : angle 1.60312 ( 3) hydrogen bonds : bond 0.04353 ( 451) hydrogen bonds : angle 5.11477 ( 1242) SS BOND : bond 0.00233 ( 12) SS BOND : angle 2.33242 ( 24) covalent geometry : bond 0.00523 (14141) covalent geometry : angle 0.59438 (19225) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8626 (t0) cc_final: 0.8216 (t0) REVERT: A 147 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8093 (mtm-85) REVERT: A 536 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8324 (mttm) REVERT: A 538 LYS cc_start: 0.8250 (mtpm) cc_final: 0.7881 (mttp) REVERT: A 591 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.7737 (tpp) REVERT: A 616 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8244 (mtt) REVERT: A 660 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.7655 (mp0) REVERT: C 71 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8607 (tttm) REVERT: C 83 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.7229 (p90) REVERT: C 98 PHE cc_start: 0.6356 (OUTLIER) cc_final: 0.5102 (m-80) REVERT: C 336 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7949 (mtp-110) REVERT: C 391 LYS cc_start: 0.7703 (ttmm) cc_final: 0.7176 (ttpt) REVERT: C 503 MET cc_start: 0.8805 (mtp) cc_final: 0.8521 (mtp) REVERT: C 536 LYS cc_start: 0.8350 (mtmm) cc_final: 0.7839 (mmtt) REVERT: C 615 LYS cc_start: 0.8106 (ttpt) cc_final: 0.7759 (pttt) REVERT: B 509 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8423 (ptpt) outliers start: 36 outliers final: 19 residues processed: 182 average time/residue: 1.2857 time to fit residues: 255.9936 Evaluate side-chains 183 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 98 PHE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 83 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 138 ASN A 141 GLN A 506 ASN A 621 ASN C 51 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 533 HIS C 761 GLN B 406 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.123018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.091786 restraints weight = 14905.625| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 1.64 r_work: 0.2692 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8957 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14180 Z= 0.200 Angle : 0.603 10.231 19330 Z= 0.313 Chirality : 0.047 0.407 2115 Planarity : 0.004 0.059 2411 Dihedral : 5.317 51.883 2395 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.25 % Allowed : 18.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1637 helix: 0.20 (0.34), residues: 232 sheet: 0.14 (0.21), residues: 533 loop : -0.82 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 157 HIS 0.005 0.001 HIS C 682 PHE 0.021 0.001 PHE C 387 TYR 0.019 0.002 TYR C 752 ARG 0.004 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00246 ( 16) link_NAG-ASN : angle 2.15246 ( 48) link_BETA1-4 : bond 0.00266 ( 9) link_BETA1-4 : angle 1.67576 ( 27) link_ALPHA1-2 : bond 0.00934 ( 1) link_ALPHA1-2 : angle 1.69960 ( 3) link_ALPHA1-3 : bond 0.00793 ( 1) link_ALPHA1-3 : angle 1.49827 ( 3) hydrogen bonds : bond 0.04215 ( 451) hydrogen bonds : angle 5.12134 ( 1242) SS BOND : bond 0.00212 ( 12) SS BOND : angle 2.10644 ( 24) covalent geometry : bond 0.00483 (14141) covalent geometry : angle 0.58631 (19225) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 1.618 Fit side-chains revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8626 (t0) cc_final: 0.8263 (t0) REVERT: A 100 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.7092 (p-80) REVERT: A 147 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8078 (mtm-85) REVERT: A 536 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8319 (mttm) REVERT: A 538 LYS cc_start: 0.8231 (mtpm) cc_final: 0.7872 (mttp) REVERT: A 591 MET cc_start: 0.8975 (OUTLIER) cc_final: 0.7762 (tpp) REVERT: A 616 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8236 (mtt) REVERT: A 660 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.7673 (mp0) REVERT: C 71 LYS cc_start: 0.9006 (OUTLIER) cc_final: 0.8612 (tttm) REVERT: C 83 TYR cc_start: 0.8208 (OUTLIER) cc_final: 0.7131 (p90) REVERT: C 336 ARG cc_start: 0.8194 (mtp-110) cc_final: 0.7920 (mtp-110) REVERT: C 391 LYS cc_start: 0.7693 (ttmm) cc_final: 0.7151 (ttpt) REVERT: C 503 MET cc_start: 0.8792 (mtp) cc_final: 0.8516 (mtp) REVERT: C 536 LYS cc_start: 0.8346 (mtmm) cc_final: 0.7833 (mmtt) REVERT: C 615 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7736 (pttt) REVERT: B 509 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8377 (ptpt) outliers start: 33 outliers final: 19 residues processed: 183 average time/residue: 1.3845 time to fit residues: 277.5354 Evaluate side-chains 183 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 93 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 138 ASN A 141 GLN A 505 GLN A 506 ASN A 621 ASN C 51 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 HIS C 761 GLN B 406 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.124288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.092640 restraints weight = 14843.199| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 1.61 r_work: 0.2700 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8947 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14180 Z= 0.151 Angle : 0.571 10.534 19330 Z= 0.297 Chirality : 0.045 0.386 2115 Planarity : 0.004 0.059 2411 Dihedral : 5.157 45.394 2395 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.91 % Allowed : 19.28 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1637 helix: 0.30 (0.34), residues: 228 sheet: 0.15 (0.21), residues: 533 loop : -0.84 (0.20), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 157 HIS 0.004 0.001 HIS C 748 PHE 0.021 0.001 PHE A 387 TYR 0.018 0.001 TYR C 752 ARG 0.004 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00213 ( 16) link_NAG-ASN : angle 2.05757 ( 48) link_BETA1-4 : bond 0.00264 ( 9) link_BETA1-4 : angle 1.61586 ( 27) link_ALPHA1-2 : bond 0.00946 ( 1) link_ALPHA1-2 : angle 1.63202 ( 3) link_ALPHA1-3 : bond 0.00844 ( 1) link_ALPHA1-3 : angle 1.41209 ( 3) hydrogen bonds : bond 0.03896 ( 451) hydrogen bonds : angle 5.05384 ( 1242) SS BOND : bond 0.00174 ( 12) SS BOND : angle 1.97151 ( 24) covalent geometry : bond 0.00359 (14141) covalent geometry : angle 0.55526 (19225) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3274 Ramachandran restraints generated. 1637 Oldfield, 0 Emsley, 1637 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8623 (t0) cc_final: 0.8254 (t0) REVERT: A 100 HIS cc_start: 0.7300 (OUTLIER) cc_final: 0.6949 (p-80) REVERT: A 147 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8069 (mtm-85) REVERT: A 536 LYS cc_start: 0.8597 (mtpp) cc_final: 0.8325 (mttm) REVERT: A 538 LYS cc_start: 0.8248 (mtpm) cc_final: 0.7891 (mttp) REVERT: A 591 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.7786 (tpp) REVERT: A 616 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8203 (mtt) REVERT: A 660 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: C 83 TYR cc_start: 0.8191 (OUTLIER) cc_final: 0.7134 (p90) REVERT: C 336 ARG cc_start: 0.8174 (mtp-110) cc_final: 0.7895 (mtp-110) REVERT: C 391 LYS cc_start: 0.7666 (ttmm) cc_final: 0.7121 (ttpt) REVERT: C 503 MET cc_start: 0.8798 (mtp) cc_final: 0.8518 (mtp) REVERT: C 536 LYS cc_start: 0.8350 (mtmm) cc_final: 0.7838 (mmtt) REVERT: C 615 LYS cc_start: 0.8098 (ttpt) cc_final: 0.7733 (pttt) REVERT: B 509 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8358 (ptpt) outliers start: 28 outliers final: 20 residues processed: 174 average time/residue: 1.2933 time to fit residues: 246.2140 Evaluate side-chains 182 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 100 HIS Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 147 ARG Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain A residue 627 TRP Chi-restraints excluded: chain A residue 660 GLU Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 83 TYR Chi-restraints excluded: chain C residue 100 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 726 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 424 SER Chi-restraints excluded: chain B residue 509 LYS Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 582 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 75 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 133 optimal weight: 0.7980 chunk 142 optimal weight: 0.0370 chunk 51 optimal weight: 6.9990 chunk 159 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 138 ASN A 141 GLN A 506 ASN A 621 ASN C 51 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 533 HIS C 606 GLN C 761 GLN B 406 ASN ** B 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.094798 restraints weight = 14937.150| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 1.55 r_work: 0.2755 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 14180 Z= 0.107 Angle : 0.523 10.766 19330 Z= 0.273 Chirality : 0.044 0.351 2115 Planarity : 0.004 0.060 2411 Dihedral : 4.711 30.575 2395 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.63 % Allowed : 19.48 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.20), residues: 1637 helix: 0.38 (0.34), residues: 236 sheet: 0.26 (0.22), residues: 521 loop : -0.77 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 124 HIS 0.005 0.001 HIS C 748 PHE 0.021 0.001 PHE A 387 TYR 0.017 0.001 TYR C 752 ARG 0.004 0.000 ARG A 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 16) link_NAG-ASN : angle 1.82812 ( 48) link_BETA1-4 : bond 0.00301 ( 9) link_BETA1-4 : angle 1.47937 ( 27) link_ALPHA1-2 : bond 0.00972 ( 1) link_ALPHA1-2 : angle 1.50550 ( 3) link_ALPHA1-3 : bond 0.00850 ( 1) link_ALPHA1-3 : angle 1.33451 ( 3) hydrogen bonds : bond 0.03359 ( 451) hydrogen bonds : angle 4.88043 ( 1242) SS BOND : bond 0.00167 ( 12) SS BOND : angle 1.59701 ( 24) covalent geometry : bond 0.00247 (14141) covalent geometry : angle 0.50989 (19225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10058.02 seconds wall clock time: 172 minutes 8.02 seconds (10328.02 seconds total)