Starting phenix.real_space_refine on Thu Sep 18 03:27:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jmm_61606/09_2025/9jmm_61606.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jmm_61606/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jmm_61606/09_2025/9jmm_61606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jmm_61606/09_2025/9jmm_61606.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jmm_61606/09_2025/9jmm_61606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jmm_61606/09_2025/9jmm_61606.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.152 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 3.49, per 1000 atoms: 0.25 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: 1.35 Conformation dependent library (CDL) restraints added in 633.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.73 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: 2.81 Time building geometry restraints manager: 1.68 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: 1.110 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.850 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (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 ARG 0.006 0.001 ARG A 310 TYR 0.030 0.002 TYR C 468 PHE 0.025 0.001 PHE C 461 TRP 0.020 0.002 TRP A 201 HIS 0.011 0.001 HIS A 704 Details of bonding type rmsd covalent geometry : bond 0.00840 (14141) covalent geometry : angle 0.90404 (19225) SS BOND : bond 0.00533 ( 12) SS BOND : angle 1.69724 ( 24) hydrogen bonds : bond 0.20224 ( 451) hydrogen bonds : angle 7.31298 ( 1242) 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) link_BETA1-4 : bond 0.00303 ( 9) link_BETA1-4 : angle 1.50830 ( 27) link_NAG-ASN : bond 0.00240 ( 16) link_NAG-ASN : angle 2.31034 ( 48) *********************** 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 : 0.540 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: 0.6908 time to fit residues: 134.7230 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 : 0.631 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.3364 r_free = 0.3364 target = 0.124792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.093682 restraints weight = 14796.802| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 1.69 r_work: 0.2722 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14180 Z= 0.177 Angle : 0.598 11.198 19330 Z= 0.315 Chirality : 0.047 0.414 2115 Planarity : 0.004 0.062 2411 Dihedral : 7.952 77.127 2407 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.52 % Allowed : 17.64 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.20), residues: 1637 helix: -0.22 (0.32), residues: 248 sheet: 0.24 (0.21), residues: 535 loop : -0.81 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 54 TYR 0.018 0.002 TYR A 256 PHE 0.020 0.001 PHE C 387 TRP 0.012 0.002 TRP C 157 HIS 0.004 0.001 HIS C 748 Details of bonding type rmsd covalent geometry : bond 0.00415 (14141) covalent geometry : angle 0.58518 (19225) SS BOND : bond 0.00205 ( 12) SS BOND : angle 1.34024 ( 24) hydrogen bonds : bond 0.04814 ( 451) hydrogen bonds : angle 5.50904 ( 1242) link_ALPHA1-2 : bond 0.00971 ( 1) link_ALPHA1-2 : angle 1.76309 ( 3) link_ALPHA1-3 : bond 0.01195 ( 1) link_ALPHA1-3 : angle 1.83624 ( 3) link_BETA1-4 : bond 0.00415 ( 9) link_BETA1-4 : angle 1.48673 ( 27) link_NAG-ASN : bond 0.00232 ( 16) link_NAG-ASN : angle 2.02792 ( 48) *********************** 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 199 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.596 Fit side-chains REVERT: A 489 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8424 (tttm) REVERT: A 538 LYS cc_start: 0.8133 (mtpm) cc_final: 0.7825 (mttp) REVERT: A 589 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8184 (tttm) REVERT: A 591 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8749 (ttp) REVERT: A 621 ASN cc_start: 0.7836 (m110) cc_final: 0.7604 (m-40) REVERT: C 71 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8496 (tttm) REVERT: C 98 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6571 (m-80) REVERT: C 191 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: B 576 GLU cc_start: 0.8237 (mp0) cc_final: 0.8033 (mp0) outliers start: 37 outliers final: 10 residues processed: 189 average time/residue: 0.6607 time to fit residues: 136.6614 Evaluate side-chains 174 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.555 ------------------------------------------------------------------------------- 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 489 LYS Chi-restraints excluded: chain A residue 518 ILE 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 71 LYS Chi-restraints excluded: chain C residue 98 PHE 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 334 SER 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 156 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 152 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 158 optimal weight: 0.0270 chunk 63 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.9242 ------------------------------------------------------------------------------- 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 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.124430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.093524 restraints weight = 14922.306| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.64 r_work: 0.2734 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14180 Z= 0.160 Angle : 0.569 11.108 19330 Z= 0.296 Chirality : 0.046 0.514 2115 Planarity : 0.004 0.061 2411 Dihedral : 6.732 58.113 2398 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.79 % Allowed : 17.23 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.20), residues: 1637 helix: -0.10 (0.33), residues: 248 sheet: 0.18 (0.21), residues: 536 loop : -0.82 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 336 TYR 0.018 0.002 TYR C 752 PHE 0.022 0.001 PHE C 387 TRP 0.013 0.002 TRP C 157 HIS 0.004 0.001 HIS C 748 Details of bonding type rmsd covalent geometry : bond 0.00377 (14141) covalent geometry : angle 0.55509 (19225) SS BOND : bond 0.00178 ( 12) SS BOND : angle 1.18894 ( 24) hydrogen bonds : bond 0.04287 ( 451) hydrogen bonds : angle 5.20404 ( 1242) link_ALPHA1-2 : bond 0.00919 ( 1) link_ALPHA1-2 : angle 1.71239 ( 3) link_ALPHA1-3 : bond 0.01184 ( 1) link_ALPHA1-3 : angle 1.56452 ( 3) link_BETA1-4 : bond 0.00294 ( 9) link_BETA1-4 : angle 1.54666 ( 27) link_NAG-ASN : bond 0.00144 ( 16) link_NAG-ASN : angle 2.15747 ( 48) *********************** 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 194 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.550 Fit side-chains REVERT: A 147 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8080 (mtm-85) REVERT: A 538 LYS cc_start: 0.8185 (mtpm) cc_final: 0.7874 (mttp) REVERT: A 589 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8232 (tttm) REVERT: A 591 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8712 (ttp) REVERT: A 621 ASN cc_start: 0.7817 (m110) cc_final: 0.7592 (m-40) REVERT: C 71 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8476 (tttm) REVERT: C 336 ARG cc_start: 0.8195 (mtp-110) cc_final: 0.7994 (mtp-110) outliers start: 41 outliers final: 15 residues processed: 180 average time/residue: 0.6522 time to fit residues: 128.5693 Evaluate side-chains 170 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.564 ------------------------------------------------------------------------------- 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 312 SER Chi-restraints excluded: chain A residue 518 ILE 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 486 VAL Chi-restraints excluded: chain C residue 726 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 54 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 103 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- 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 505 GLN 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 = 0.3331 r_free = 0.3331 target = 0.122289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.090715 restraints weight = 14898.573| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 1.62 r_work: 0.2681 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 14180 Z= 0.259 Angle : 0.649 10.485 19330 Z= 0.336 Chirality : 0.049 0.455 2115 Planarity : 0.005 0.061 2411 Dihedral : 6.612 58.076 2396 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.00 % Allowed : 17.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.20), residues: 1637 helix: -0.24 (0.33), residues: 246 sheet: 0.12 (0.21), residues: 534 loop : -0.88 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 492 TYR 0.020 0.002 TYR A 256 PHE 0.024 0.002 PHE C 387 TRP 0.016 0.002 TRP A 201 HIS 0.006 0.001 HIS C 682 Details of bonding type rmsd covalent geometry : bond 0.00630 (14141) covalent geometry : angle 0.63352 (19225) SS BOND : bond 0.00244 ( 12) SS BOND : angle 1.50209 ( 24) hydrogen bonds : bond 0.04822 ( 451) hydrogen bonds : angle 5.33169 ( 1242) link_ALPHA1-2 : bond 0.00875 ( 1) link_ALPHA1-2 : angle 1.86948 ( 3) link_ALPHA1-3 : bond 0.00967 ( 1) link_ALPHA1-3 : angle 1.81038 ( 3) link_BETA1-4 : bond 0.00278 ( 9) link_BETA1-4 : angle 1.76979 ( 27) link_NAG-ASN : bond 0.00289 ( 16) link_NAG-ASN : angle 2.34821 ( 48) *********************** 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 201 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.565 Fit side-chains REVERT: A 147 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8079 (mtm-85) REVERT: A 538 LYS cc_start: 0.8231 (mtpm) cc_final: 0.7880 (mttp) REVERT: A 591 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8636 (ttp) REVERT: A 660 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.7728 (mp0) REVERT: C 71 LYS cc_start: 0.9009 (OUTLIER) cc_final: 0.8583 (tttm) REVERT: C 83 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.7210 (p90) REVERT: C 336 ARG cc_start: 0.8247 (mtp-110) cc_final: 0.8032 (mtp-110) REVERT: C 536 LYS cc_start: 0.8326 (mtmm) cc_final: 0.7816 (mmtt) REVERT: B 576 GLU cc_start: 0.8335 (mp0) cc_final: 0.8123 (mp0) outliers start: 44 outliers final: 17 residues processed: 184 average time/residue: 0.6729 time to fit residues: 135.3167 Evaluate side-chains 176 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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 188 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 341 VAL 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 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 334 SER Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 690 SER 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 135 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 621 ASN C 51 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 GLN 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 = 0.3346 r_free = 0.3346 target = 0.123376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.092605 restraints weight = 14943.582| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.55 r_work: 0.2737 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8949 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14180 Z= 0.163 Angle : 0.570 10.733 19330 Z= 0.296 Chirality : 0.046 0.394 2115 Planarity : 0.004 0.061 2411 Dihedral : 6.107 59.002 2395 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.72 % Allowed : 17.98 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.20), residues: 1637 helix: -0.13 (0.33), residues: 246 sheet: 0.11 (0.21), residues: 534 loop : -0.87 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 492 TYR 0.018 0.002 TYR C 752 PHE 0.022 0.001 PHE C 387 TRP 0.014 0.002 TRP C 157 HIS 0.004 0.001 HIS C 682 Details of bonding type rmsd covalent geometry : bond 0.00384 (14141) covalent geometry : angle 0.55574 (19225) SS BOND : bond 0.00226 ( 12) SS BOND : angle 1.27932 ( 24) hydrogen bonds : bond 0.04074 ( 451) hydrogen bonds : angle 5.14911 ( 1242) link_ALPHA1-2 : bond 0.00974 ( 1) link_ALPHA1-2 : angle 1.65093 ( 3) link_ALPHA1-3 : bond 0.00993 ( 1) link_ALPHA1-3 : angle 1.67370 ( 3) link_BETA1-4 : bond 0.00284 ( 9) link_BETA1-4 : angle 1.66848 ( 27) link_NAG-ASN : bond 0.00211 ( 16) link_NAG-ASN : angle 2.13071 ( 48) *********************** 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 196 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.564 Fit side-chains REVERT: A 54 ARG cc_start: 0.8318 (mtt-85) cc_final: 0.8034 (mtt-85) REVERT: A 100 HIS cc_start: 0.7301 (OUTLIER) cc_final: 0.6917 (p-80) REVERT: A 147 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8066 (mtm-85) REVERT: A 538 LYS cc_start: 0.8237 (mtpm) cc_final: 0.7898 (mttp) REVERT: A 589 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8188 (tttm) REVERT: A 591 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8678 (ttp) REVERT: A 616 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8242 (mtt) REVERT: A 660 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: C 83 TYR cc_start: 0.8132 (OUTLIER) cc_final: 0.7114 (p90) REVERT: C 336 ARG cc_start: 0.8207 (mtp-110) cc_final: 0.7982 (mtp-110) REVERT: C 503 MET cc_start: 0.8813 (mtp) cc_final: 0.8529 (mtp) REVERT: C 536 LYS cc_start: 0.8314 (mtmm) cc_final: 0.7815 (mmtt) REVERT: B 576 GLU cc_start: 0.8294 (mp0) cc_final: 0.8093 (mp0) outliers start: 40 outliers final: 19 residues processed: 183 average time/residue: 0.6566 time to fit residues: 131.3479 Evaluate side-chains 177 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 100 HIS 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 312 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 614 SER 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 376 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 13 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 138 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 621 ASN C 51 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.123365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.091196 restraints weight = 14874.142| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.64 r_work: 0.2713 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14180 Z= 0.176 Angle : 0.583 10.506 19330 Z= 0.302 Chirality : 0.047 0.554 2115 Planarity : 0.004 0.060 2411 Dihedral : 5.525 52.307 2395 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.93 % Allowed : 17.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.20), residues: 1637 helix: -0.11 (0.33), residues: 246 sheet: 0.12 (0.21), residues: 534 loop : -0.86 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 471 TYR 0.019 0.002 TYR C 752 PHE 0.022 0.001 PHE A 387 TRP 0.014 0.002 TRP C 157 HIS 0.005 0.001 HIS C 748 Details of bonding type rmsd covalent geometry : bond 0.00421 (14141) covalent geometry : angle 0.56513 (19225) SS BOND : bond 0.00243 ( 12) SS BOND : angle 1.64004 ( 24) hydrogen bonds : bond 0.04133 ( 451) hydrogen bonds : angle 5.12349 ( 1242) link_ALPHA1-2 : bond 0.00949 ( 1) link_ALPHA1-2 : angle 1.68898 ( 3) link_ALPHA1-3 : bond 0.00925 ( 1) link_ALPHA1-3 : angle 1.79042 ( 3) link_BETA1-4 : bond 0.00301 ( 9) link_BETA1-4 : angle 1.71441 ( 27) link_NAG-ASN : bond 0.00160 ( 16) link_NAG-ASN : angle 2.39974 ( 48) *********************** 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 195 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.586 Fit side-chains revert: symmetry clash REVERT: A 54 ARG cc_start: 0.8378 (mtt-85) cc_final: 0.8105 (mtt-85) REVERT: A 147 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8090 (mtm-85) REVERT: A 538 LYS cc_start: 0.8247 (mtpm) cc_final: 0.7895 (mttp) REVERT: A 591 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8701 (ttp) REVERT: A 616 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8251 (mtt) REVERT: A 660 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: C 71 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8608 (tttm) REVERT: C 83 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7219 (p90) REVERT: C 336 ARG cc_start: 0.8236 (mtp-110) cc_final: 0.8015 (mtp-110) REVERT: C 503 MET cc_start: 0.8832 (mtp) cc_final: 0.8564 (mtp) REVERT: C 536 LYS cc_start: 0.8364 (mtmm) cc_final: 0.7853 (mmtt) REVERT: C 699 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8320 (mt-10) outliers start: 43 outliers final: 21 residues processed: 179 average time/residue: 0.6849 time to fit residues: 133.6827 Evaluate side-chains 179 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 312 SER 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 614 SER 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 376 SER Chi-restraints excluded: chain C residue 419 SER Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain B residue 572 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 148 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 102 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- 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 621 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN B 406 ASN B 476 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.091787 restraints weight = 14876.448| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.63 r_work: 0.2701 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14180 Z= 0.161 Angle : 0.567 10.318 19330 Z= 0.294 Chirality : 0.046 0.500 2115 Planarity : 0.004 0.060 2411 Dihedral : 5.205 40.645 2395 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.93 % Allowed : 18.05 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.20), residues: 1637 helix: -0.10 (0.33), residues: 248 sheet: 0.14 (0.21), residues: 534 loop : -0.84 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 471 TYR 0.018 0.002 TYR C 752 PHE 0.022 0.001 PHE A 387 TRP 0.014 0.002 TRP C 157 HIS 0.005 0.001 HIS C 748 Details of bonding type rmsd covalent geometry : bond 0.00382 (14141) covalent geometry : angle 0.55076 (19225) SS BOND : bond 0.00198 ( 12) SS BOND : angle 1.43223 ( 24) hydrogen bonds : bond 0.03967 ( 451) hydrogen bonds : angle 5.05802 ( 1242) link_ALPHA1-2 : bond 0.00958 ( 1) link_ALPHA1-2 : angle 1.64719 ( 3) link_ALPHA1-3 : bond 0.00914 ( 1) link_ALPHA1-3 : angle 1.58780 ( 3) link_BETA1-4 : bond 0.00278 ( 9) link_BETA1-4 : angle 1.66380 ( 27) link_NAG-ASN : bond 0.00217 ( 16) link_NAG-ASN : angle 2.25610 ( 48) *********************** 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 199 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 0.554 Fit side-chains REVERT: A 100 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.7114 (p-80) REVERT: A 147 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8066 (mtm-85) REVERT: A 538 LYS cc_start: 0.8221 (mtpm) cc_final: 0.7857 (mttp) REVERT: A 589 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8208 (tttm) REVERT: A 591 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8702 (ttp) REVERT: A 616 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8242 (mtt) REVERT: A 660 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: C 71 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8598 (tttm) REVERT: C 83 TYR cc_start: 0.8170 (OUTLIER) cc_final: 0.7193 (p90) REVERT: C 336 ARG cc_start: 0.8233 (mtp-110) cc_final: 0.7999 (mtp-110) REVERT: C 391 LYS cc_start: 0.7759 (ttmm) cc_final: 0.7211 (ttpt) REVERT: C 503 MET cc_start: 0.8797 (mtp) cc_final: 0.8518 (mtp) REVERT: C 536 LYS cc_start: 0.8348 (mtmm) cc_final: 0.7830 (mmtt) outliers start: 43 outliers final: 23 residues processed: 185 average time/residue: 0.6651 time to fit residues: 134.4455 Evaluate side-chains 182 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 176 ILE Chi-restraints excluded: chain A residue 312 SER 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 614 SER 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 239 SER 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 443 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 726 VAL 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 71 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 21 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 146 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- 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 621 ASN C 51 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.123760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.092545 restraints weight = 14849.857| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 1.60 r_work: 0.2703 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8945 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14180 Z= 0.142 Angle : 0.551 10.443 19330 Z= 0.287 Chirality : 0.045 0.462 2115 Planarity : 0.004 0.060 2411 Dihedral : 4.982 34.462 2395 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.45 % Allowed : 18.80 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.20), residues: 1637 helix: 0.02 (0.33), residues: 242 sheet: 0.16 (0.21), residues: 534 loop : -0.86 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 471 TYR 0.018 0.001 TYR C 752 PHE 0.021 0.001 PHE A 387 TRP 0.014 0.002 TRP C 157 HIS 0.005 0.001 HIS C 748 Details of bonding type rmsd covalent geometry : bond 0.00334 (14141) covalent geometry : angle 0.53583 (19225) SS BOND : bond 0.00245 ( 12) SS BOND : angle 1.31600 ( 24) hydrogen bonds : bond 0.03777 ( 451) hydrogen bonds : angle 4.99475 ( 1242) link_ALPHA1-2 : bond 0.00952 ( 1) link_ALPHA1-2 : angle 1.62490 ( 3) link_ALPHA1-3 : bond 0.00882 ( 1) link_ALPHA1-3 : angle 1.46467 ( 3) link_BETA1-4 : bond 0.00281 ( 9) link_BETA1-4 : angle 1.59773 ( 27) link_NAG-ASN : bond 0.00200 ( 16) link_NAG-ASN : angle 2.12952 ( 48) *********************** 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 190 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8523 (t0) cc_final: 0.7960 (t0) REVERT: A 54 ARG cc_start: 0.8406 (mtt-85) cc_final: 0.7676 (mtt-85) REVERT: A 100 HIS cc_start: 0.7401 (OUTLIER) cc_final: 0.7069 (p-80) REVERT: A 147 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8057 (mtm-85) REVERT: A 538 LYS cc_start: 0.8279 (mtpm) cc_final: 0.7916 (mttp) REVERT: A 589 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8201 (tttm) REVERT: A 591 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8710 (ttp) REVERT: A 616 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8218 (mtt) REVERT: A 660 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: C 71 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8584 (tttm) REVERT: C 83 TYR cc_start: 0.8163 (OUTLIER) cc_final: 0.7204 (p90) REVERT: C 336 ARG cc_start: 0.8231 (mtp-110) cc_final: 0.7984 (mtp-110) REVERT: C 391 LYS cc_start: 0.7675 (ttmm) cc_final: 0.7123 (ttpt) REVERT: C 503 MET cc_start: 0.8794 (mtp) cc_final: 0.8508 (mtp) REVERT: C 536 LYS cc_start: 0.8341 (mtmm) cc_final: 0.7825 (mmtt) outliers start: 36 outliers final: 21 residues processed: 180 average time/residue: 0.6677 time to fit residues: 131.5037 Evaluate side-chains 180 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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 176 ILE Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 312 SER 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 518 ILE 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 100 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 307 THR 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 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 53 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 C 51 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.123879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.092154 restraints weight = 14935.717| |-----------------------------------------------------------------------------| r_work (start): 0.2913 rms_B_bonded: 1.62 r_work: 0.2773 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14180 Z= 0.149 Angle : 0.558 10.332 19330 Z= 0.289 Chirality : 0.045 0.440 2115 Planarity : 0.004 0.060 2411 Dihedral : 4.896 34.049 2395 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.86 % Allowed : 18.53 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.20), residues: 1637 helix: 0.06 (0.33), residues: 240 sheet: 0.17 (0.21), residues: 534 loop : -0.84 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 471 TYR 0.018 0.001 TYR C 752 PHE 0.021 0.001 PHE A 387 TRP 0.013 0.002 TRP C 157 HIS 0.005 0.001 HIS C 748 Details of bonding type rmsd covalent geometry : bond 0.00353 (14141) covalent geometry : angle 0.54341 (19225) SS BOND : bond 0.00179 ( 12) SS BOND : angle 1.30018 ( 24) hydrogen bonds : bond 0.03828 ( 451) hydrogen bonds : angle 4.97170 ( 1242) link_ALPHA1-2 : bond 0.00924 ( 1) link_ALPHA1-2 : angle 1.63434 ( 3) link_ALPHA1-3 : bond 0.00860 ( 1) link_ALPHA1-3 : angle 1.45693 ( 3) link_BETA1-4 : bond 0.00275 ( 9) link_BETA1-4 : angle 1.58804 ( 27) link_NAG-ASN : bond 0.00206 ( 16) link_NAG-ASN : angle 2.09445 ( 48) *********************** 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 198 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 156 time to evaluate : 0.557 Fit side-chains revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8536 (t0) cc_final: 0.7992 (t0) REVERT: A 54 ARG cc_start: 0.8464 (mtt-85) cc_final: 0.7829 (mtt-85) REVERT: A 91 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.6956 (mp0) REVERT: A 100 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.7154 (p-80) REVERT: A 147 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8057 (mtm-85) REVERT: A 538 LYS cc_start: 0.8340 (mtpm) cc_final: 0.8009 (mttp) REVERT: A 589 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8175 (tttm) REVERT: A 591 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8657 (ttp) REVERT: A 616 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8244 (mtt) REVERT: A 660 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: C 71 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8578 (tttm) REVERT: C 83 TYR cc_start: 0.8177 (OUTLIER) cc_final: 0.7235 (p90) REVERT: C 141 GLN cc_start: 0.8657 (pt0) cc_final: 0.8373 (pt0) REVERT: C 336 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.7982 (mtp-110) REVERT: C 391 LYS cc_start: 0.7724 (ttmm) cc_final: 0.7207 (ttpt) REVERT: C 503 MET cc_start: 0.8815 (mtp) cc_final: 0.8525 (mtp) REVERT: C 536 LYS cc_start: 0.8358 (mtmm) cc_final: 0.7878 (mmtt) REVERT: C 615 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7758 (pttt) outliers start: 42 outliers final: 22 residues processed: 186 average time/residue: 0.6850 time to fit residues: 138.8978 Evaluate side-chains 184 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 188 THR Chi-restraints excluded: chain A residue 312 SER 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 518 ILE 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 100 HIS Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 239 SER 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 443 THR Chi-restraints excluded: chain C residue 486 VAL Chi-restraints excluded: chain C residue 726 VAL 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 113 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 138 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 52 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.0070 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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 621 ASN C 51 ASN ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.125739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.094668 restraints weight = 14881.478| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 1.61 r_work: 0.2746 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14180 Z= 0.103 Angle : 0.509 10.668 19330 Z= 0.265 Chirality : 0.044 0.399 2115 Planarity : 0.004 0.060 2411 Dihedral : 4.581 30.224 2395 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.84 % Allowed : 19.48 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.20), residues: 1637 helix: 0.35 (0.34), residues: 237 sheet: 0.28 (0.22), residues: 522 loop : -0.76 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 471 TYR 0.017 0.001 TYR C 752 PHE 0.021 0.001 PHE A 387 TRP 0.017 0.001 TRP C 124 HIS 0.006 0.001 HIS C 748 Details of bonding type rmsd covalent geometry : bond 0.00234 (14141) covalent geometry : angle 0.49688 (19225) SS BOND : bond 0.00137 ( 12) SS BOND : angle 1.06555 ( 24) hydrogen bonds : bond 0.03289 ( 451) hydrogen bonds : angle 4.82405 ( 1242) link_ALPHA1-2 : bond 0.00943 ( 1) link_ALPHA1-2 : angle 1.51154 ( 3) link_ALPHA1-3 : bond 0.00881 ( 1) link_ALPHA1-3 : angle 1.38592 ( 3) link_BETA1-4 : bond 0.00303 ( 9) link_BETA1-4 : angle 1.45172 ( 27) link_NAG-ASN : bond 0.00199 ( 16) link_NAG-ASN : angle 1.88681 ( 48) ********************** 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 186 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 0.553 Fit side-chains revert: symmetry clash REVERT: A 51 ASN cc_start: 0.8479 (t0) cc_final: 0.7951 (t0) REVERT: A 54 ARG cc_start: 0.8455 (mtt-85) cc_final: 0.7800 (mtt-85) REVERT: A 91 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: A 538 LYS cc_start: 0.8294 (mtpm) cc_final: 0.7932 (mttp) REVERT: A 616 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8143 (mtt) REVERT: C 41 LYS cc_start: 0.8622 (mtmt) cc_final: 0.7620 (tttp) REVERT: C 83 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7164 (p90) REVERT: C 141 GLN cc_start: 0.8595 (pt0) cc_final: 0.8322 (pt0) REVERT: C 336 ARG cc_start: 0.8200 (mtp-110) cc_final: 0.7930 (mtp-110) REVERT: C 378 GLU cc_start: 0.7917 (mp0) cc_final: 0.7622 (mp0) REVERT: C 391 LYS cc_start: 0.7580 (ttmm) cc_final: 0.6875 (tmtm) REVERT: C 503 MET cc_start: 0.8783 (mtp) cc_final: 0.8517 (mtp) REVERT: C 536 LYS cc_start: 0.8347 (mtmm) cc_final: 0.7836 (mmtt) REVERT: C 615 LYS cc_start: 0.8049 (ttpt) cc_final: 0.7713 (pttt) outliers start: 27 outliers final: 20 residues processed: 179 average time/residue: 0.6586 time to fit residues: 129.0633 Evaluate side-chains 176 residues out of total 1468 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 101 SER Chi-restraints excluded: chain A residue 188 THR Chi-restraints excluded: chain A residue 312 SER Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 616 MET 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 239 SER Chi-restraints excluded: chain C residue 243 ASP 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 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 10 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 147 optimal weight: 20.0000 chunk 123 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 621 ASN ** C 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 GLN C 533 HIS C 761 GLN ** 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 = 0.3375 r_free = 0.3375 target = 0.125689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.094285 restraints weight = 14848.129| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.61 r_work: 0.2748 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8912 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 14180 Z= 0.162 Angle : 0.764 61.599 19330 Z= 0.373 Chirality : 0.046 0.469 2115 Planarity : 0.004 0.060 2411 Dihedral : 4.582 30.294 2395 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.50 % Allowed : 20.10 % Favored : 78.41 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.20), residues: 1637 helix: 0.34 (0.34), residues: 237 sheet: 0.29 (0.22), residues: 522 loop : -0.74 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 461 TYR 0.017 0.001 TYR C 752 PHE 0.020 0.001 PHE A 387 TRP 0.014 0.002 TRP C 124 HIS 0.006 0.001 HIS C 748 Details of bonding type rmsd covalent geometry : bond 0.00360 (14141) covalent geometry : angle 0.75695 (19225) SS BOND : bond 0.00155 ( 12) SS BOND : angle 1.06043 ( 24) hydrogen bonds : bond 0.03361 ( 451) hydrogen bonds : angle 4.82352 ( 1242) link_ALPHA1-2 : bond 0.00956 ( 1) link_ALPHA1-2 : angle 1.51469 ( 3) link_ALPHA1-3 : bond 0.00838 ( 1) link_ALPHA1-3 : angle 1.38961 ( 3) link_BETA1-4 : bond 0.00309 ( 9) link_BETA1-4 : angle 1.46221 ( 27) link_NAG-ASN : bond 0.00211 ( 16) link_NAG-ASN : angle 1.87716 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5361.41 seconds wall clock time: 92 minutes 25.52 seconds (5545.52 seconds total)