Starting phenix.real_space_refine on Fri Mar 6 23:48:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7r7t_24304/03_2026/7r7t_24304.cif Found real_map, /net/cci-nas-00/data/ceres_data/7r7t_24304/03_2026/7r7t_24304.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7r7t_24304/03_2026/7r7t_24304.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7r7t_24304/03_2026/7r7t_24304.map" model { file = "/net/cci-nas-00/data/ceres_data/7r7t_24304/03_2026/7r7t_24304.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7r7t_24304/03_2026/7r7t_24304.cif" } resolution = 4.5 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= 0.025 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: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 182 5.16 5 C 22167 2.51 5 N 6282 2.21 5 O 6696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35351 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5724 Classifications: {'peptide': 729} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 688} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 5707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 5707 Classifications: {'peptide': 725} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 683} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 5692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5692 Classifications: {'peptide': 726} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 685} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 5686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5686 Classifications: {'peptide': 724} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 683} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 5736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5736 Classifications: {'peptide': 731} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 689} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 5704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 727, 5704 Classifications: {'peptide': 727} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 686} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "I" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 778 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.67, per 1000 atoms: 0.22 Number of scatterers: 35351 At special positions: 0 Unit cell: (132.822, 170.973, 166.734, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 182 16.00 P 24 15.00 O 6696 8.00 N 6282 7.00 C 22167 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.82 Conformation dependent library (CDL) restraints added in 1.3 seconds 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8380 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 34 sheets defined 41.9% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 42 through 49 Processing helix chain 'A' and resid 61 through 65 removed outlier: 3.998A pdb=" N ARG A 64 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 209 through 221 removed outlier: 3.811A pdb=" N ALA A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N GLN A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 271 through 277 removed outlier: 3.887A pdb=" N LYS A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.727A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 removed outlier: 4.151A pdb=" N ILE A 309 " --> pdb=" O GLU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.652A pdb=" N ARG A 359 " --> pdb=" O ALA A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 379 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.258A pdb=" N HIS A 384 " --> pdb=" O ILE A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 3.701A pdb=" N ASN A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 426 Processing helix chain 'A' and resid 448 through 458 Processing helix chain 'A' and resid 482 through 499 removed outlier: 3.867A pdb=" N LEU A 489 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Proline residue: A 496 - end of helix Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 543 through 554 removed outlier: 3.654A pdb=" N MET A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 554 " --> pdb=" O MET A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 569 removed outlier: 3.939A pdb=" N ARG A 560 " --> pdb=" O GLU A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 589 removed outlier: 3.554A pdb=" N GLY A 588 " --> pdb=" O LYS A 584 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASN A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 625 through 629 removed outlier: 3.866A pdb=" N ILE A 628 " --> pdb=" O ARG A 625 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE A 629 " --> pdb=" O PRO A 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 625 through 629' Processing helix chain 'A' and resid 649 through 662 removed outlier: 4.078A pdb=" N VAL A 654 " --> pdb=" O GLU A 650 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALA A 655 " --> pdb=" O LYS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 679 Processing helix chain 'A' and resid 683 through 712 Processing helix chain 'A' and resid 732 through 740 removed outlier: 4.223A pdb=" N PHE A 736 " --> pdb=" O ARG A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 763 removed outlier: 3.803A pdb=" N ARG A 753 " --> pdb=" O ASP A 749 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR A 761 " --> pdb=" O MET A 757 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 762 " --> pdb=" O PHE A 758 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 49 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 192 through 199 removed outlier: 3.905A pdb=" N LEU F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 222 Processing helix chain 'F' and resid 228 through 234 Processing helix chain 'F' and resid 250 through 259 removed outlier: 3.660A pdb=" N ALA F 255 " --> pdb=" O LYS F 251 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 276 removed outlier: 4.365A pdb=" N ILE F 274 " --> pdb=" O ASN F 270 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N MET F 275 " --> pdb=" O GLY F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 294 Processing helix chain 'F' and resid 305 through 310 removed outlier: 3.682A pdb=" N ILE F 309 " --> pdb=" O GLU F 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 319 through 334 Processing helix chain 'F' and resid 375 through 385 Processing helix chain 'F' and resid 407 through 426 removed outlier: 4.031A pdb=" N LYS F 426 " --> pdb=" O ALA F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 444 Processing helix chain 'F' and resid 448 through 457 Processing helix chain 'F' and resid 482 through 493 Processing helix chain 'F' and resid 493 through 499 removed outlier: 4.316A pdb=" N VAL F 497 " --> pdb=" O VAL F 493 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 507 removed outlier: 3.926A pdb=" N PHE F 503 " --> pdb=" O HIS F 499 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N PHE F 506 " --> pdb=" O LYS F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 535 Processing helix chain 'F' and resid 543 through 553 Processing helix chain 'F' and resid 556 through 569 removed outlier: 3.797A pdb=" N ARG F 560 " --> pdb=" O GLU F 556 " (cutoff:3.500A) Processing helix chain 'F' and resid 579 through 587 removed outlier: 4.321A pdb=" N ALA F 583 " --> pdb=" O LEU F 579 " (cutoff:3.500A) Processing helix chain 'F' and resid 600 through 611 Processing helix chain 'F' and resid 649 through 664 removed outlier: 3.511A pdb=" N ARG F 653 " --> pdb=" O ASP F 649 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL F 654 " --> pdb=" O GLU F 650 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA F 655 " --> pdb=" O LYS F 651 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG F 662 " --> pdb=" O LYS F 658 " (cutoff:3.500A) Processing helix chain 'F' and resid 672 through 679 Processing helix chain 'F' and resid 683 through 713 Processing helix chain 'F' and resid 733 through 742 removed outlier: 3.780A pdb=" N GLU F 738 " --> pdb=" O ASP F 734 " (cutoff:3.500A) Processing helix chain 'F' and resid 748 through 760 Processing helix chain 'E' and resid 42 through 49 Processing helix chain 'E' and resid 85 through 92 removed outlier: 3.641A pdb=" N ARG E 89 " --> pdb=" O ASN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 123 removed outlier: 3.619A pdb=" N VAL E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 209 through 222 removed outlier: 4.631A pdb=" N GLN E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 234 removed outlier: 3.992A pdb=" N PHE E 230 " --> pdb=" O HIS E 226 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS E 231 " --> pdb=" O PRO E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.564A pdb=" N ALA E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 275 Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.672A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 310 removed outlier: 3.612A pdb=" N ILE E 309 " --> pdb=" O GLU E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 319 through 333 Processing helix chain 'E' and resid 373 through 385 Processing helix chain 'E' and resid 396 through 403 removed outlier: 3.635A pdb=" N ALA E 400 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR E 403 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 426 removed outlier: 3.772A pdb=" N LYS E 426 " --> pdb=" O ALA E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 458 Processing helix chain 'E' and resid 482 through 499 removed outlier: 4.696A pdb=" N TYR E 495 " --> pdb=" O GLU E 491 " (cutoff:3.500A) Proline residue: E 496 - end of helix Processing helix chain 'E' and resid 499 through 507 removed outlier: 4.242A pdb=" N PHE E 503 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 506 " --> pdb=" O LYS E 502 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 535 Processing helix chain 'E' and resid 543 through 553 Processing helix chain 'E' and resid 557 through 569 removed outlier: 4.252A pdb=" N GLU E 561 " --> pdb=" O ALA E 557 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 562 " --> pdb=" O ASN E 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 587 removed outlier: 3.938A pdb=" N ALA E 583 " --> pdb=" O LEU E 579 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG E 586 " --> pdb=" O ILE E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 600 through 610 removed outlier: 3.521A pdb=" N ILE E 604 " --> pdb=" O VAL E 600 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 605 " --> pdb=" O ILE E 601 " (cutoff:3.500A) Processing helix chain 'E' and resid 625 through 629 removed outlier: 3.746A pdb=" N ILE E 628 " --> pdb=" O ARG E 625 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE E 629 " --> pdb=" O PRO E 626 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 625 through 629' Processing helix chain 'E' and resid 649 through 662 Processing helix chain 'E' and resid 678 through 682 removed outlier: 4.562A pdb=" N GLY E 681 " --> pdb=" O MET E 678 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 713 removed outlier: 3.548A pdb=" N CYS E 691 " --> pdb=" O LEU E 687 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 732 through 742 removed outlier: 4.332A pdb=" N PHE E 742 " --> pdb=" O GLU E 738 " (cutoff:3.500A) Processing helix chain 'E' and resid 748 through 762 Processing helix chain 'D' and resid 42 through 49 removed outlier: 3.625A pdb=" N ASP D 47 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU D 48 " --> pdb=" O PRO D 44 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU D 49 " --> pdb=" O LYS D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 120 through 123 removed outlier: 3.714A pdb=" N VAL D 123 " --> pdb=" O ASP D 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 134 through 139 removed outlier: 3.631A pdb=" N TYR D 138 " --> pdb=" O TYR D 134 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 134 through 139' Processing helix chain 'D' and resid 209 through 221 removed outlier: 4.549A pdb=" N GLN D 215 " --> pdb=" O LYS D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'D' and resid 229 through 234 Processing helix chain 'D' and resid 250 through 259 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 305 through 310 removed outlier: 3.985A pdb=" N ILE D 309 " --> pdb=" O GLU D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 335 Processing helix chain 'D' and resid 354 through 359 removed outlier: 3.776A pdb=" N ARG D 359 " --> pdb=" O ALA D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 385 Processing helix chain 'D' and resid 398 through 403 removed outlier: 3.817A pdb=" N THR D 403 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 426 Processing helix chain 'D' and resid 438 through 443 Processing helix chain 'D' and resid 448 through 458 Processing helix chain 'D' and resid 482 through 499 removed outlier: 3.550A pdb=" N ARG D 487 " --> pdb=" O GLU D 483 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR D 495 " --> pdb=" O GLU D 491 " (cutoff:3.500A) Proline residue: D 496 - end of helix Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.916A pdb=" N LEU D 504 " --> pdb=" O PRO D 500 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE D 506 " --> pdb=" O LYS D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 536 Processing helix chain 'D' and resid 543 through 554 Processing helix chain 'D' and resid 557 through 569 removed outlier: 3.570A pdb=" N ALA D 569 " --> pdb=" O LYS D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 579 through 585 removed outlier: 4.274A pdb=" N ALA D 583 " --> pdb=" O LEU D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 610 Processing helix chain 'D' and resid 652 through 660 removed outlier: 4.301A pdb=" N ILE D 656 " --> pdb=" O SER D 652 " (cutoff:3.500A) Processing helix chain 'D' and resid 683 through 713 removed outlier: 3.981A pdb=" N ARG D 713 " --> pdb=" O ARG D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 742 removed outlier: 3.795A pdb=" N PHE D 736 " --> pdb=" O ARG D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 748 through 762 Processing helix chain 'C' and resid 42 through 50 removed outlier: 4.089A pdb=" N ASP C 47 " --> pdb=" O GLN C 43 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU C 48 " --> pdb=" O PRO C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 92 Processing helix chain 'C' and resid 120 through 123 Processing helix chain 'C' and resid 134 through 139 removed outlier: 3.596A pdb=" N TYR C 138 " --> pdb=" O TYR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 196 removed outlier: 3.711A pdb=" N GLU C 196 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 222 removed outlier: 4.739A pdb=" N GLN C 215 " --> pdb=" O LYS C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 234 removed outlier: 4.071A pdb=" N ALA C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 305 through 310 Processing helix chain 'C' and resid 318 through 334 removed outlier: 4.060A pdb=" N ARG C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.726A pdb=" N GLU C 402 " --> pdb=" O GLN C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 426 removed outlier: 3.819A pdb=" N LYS C 426 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 458 removed outlier: 3.552A pdb=" N PHE C 452 " --> pdb=" O THR C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 493 Processing helix chain 'C' and resid 493 through 499 removed outlier: 3.570A pdb=" N VAL C 497 " --> pdb=" O VAL C 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 536 removed outlier: 3.849A pdb=" N ALA C 530 " --> pdb=" O LEU C 526 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ILE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ALA C 532 " --> pdb=" O ALA C 528 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN C 533 " --> pdb=" O LYS C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 553 Processing helix chain 'C' and resid 557 through 569 removed outlier: 3.869A pdb=" N GLU C 561 " --> pdb=" O ALA C 557 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 588 removed outlier: 3.880A pdb=" N ILE C 582 " --> pdb=" O GLU C 578 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA C 583 " --> pdb=" O LEU C 579 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ALA C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY C 588 " --> pdb=" O LYS C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 600 through 610 Processing helix chain 'C' and resid 649 through 659 removed outlier: 4.277A pdb=" N VAL C 654 " --> pdb=" O GLU C 650 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 655 " --> pdb=" O LYS C 651 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA C 659 " --> pdb=" O ALA C 655 " (cutoff:3.500A) Processing helix chain 'C' and resid 660 through 662 No H-bonds generated for 'chain 'C' and resid 660 through 662' Processing helix chain 'C' and resid 683 through 713 removed outlier: 4.073A pdb=" N ARG C 708 " --> pdb=" O GLU C 704 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG C 709 " --> pdb=" O SER C 705 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 742 removed outlier: 4.077A pdb=" N PHE C 736 " --> pdb=" O ARG C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 748 through 762 removed outlier: 3.568A pdb=" N ILE C 752 " --> pdb=" O SER C 748 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS C 754 " --> pdb=" O ASN C 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 120 through 123 removed outlier: 3.669A pdb=" N VAL B 123 " --> pdb=" O ASP B 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 129 through 134 removed outlier: 4.071A pdb=" N VAL B 133 " --> pdb=" O ASN B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 139 Processing helix chain 'B' and resid 193 through 198 Processing helix chain 'B' and resid 209 through 221 removed outlier: 4.186A pdb=" N GLN B 215 " --> pdb=" O LYS B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 234 Processing helix chain 'B' and resid 250 through 258 Processing helix chain 'B' and resid 271 through 277 removed outlier: 3.611A pdb=" N LYS B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 305 through 310 removed outlier: 3.831A pdb=" N ILE B 309 " --> pdb=" O GLU B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 333 removed outlier: 4.040A pdb=" N ASP B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 407 through 426 removed outlier: 3.987A pdb=" N LYS B 426 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 458 Processing helix chain 'B' and resid 482 through 494 removed outlier: 3.672A pdb=" N VAL B 493 " --> pdb=" O LEU B 489 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLN B 494 " --> pdb=" O GLN B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 526 through 534 Processing helix chain 'B' and resid 543 through 553 Processing helix chain 'B' and resid 557 through 569 removed outlier: 3.703A pdb=" N GLU B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 588 removed outlier: 3.640A pdb=" N GLY B 588 " --> pdb=" O LYS B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 610 Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 674 through 679 removed outlier: 3.604A pdb=" N MET B 678 " --> pdb=" O PHE B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 713 removed outlier: 3.561A pdb=" N ARG B 713 " --> pdb=" O ARG B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.920A pdb=" N ALA B 743 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 763 Processing helix chain 'I' and resid 275 through 287 removed outlier: 3.579A pdb=" N ILE I 287 " --> pdb=" O ALA I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.712A pdb=" N LEU A 26 " --> pdb=" O ILE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 69 removed outlier: 3.595A pdb=" N VAL A 57 " --> pdb=" O CYS A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 111 Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 270 removed outlier: 6.915A pdb=" N ILE A 269 " --> pdb=" O ASP A 304 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE A 241 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR A 347 " --> pdb=" O ILE A 241 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N LEU A 243 " --> pdb=" O THR A 347 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 517 removed outlier: 6.543A pdb=" N ASN A 538 " --> pdb=" O VAL A 573 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N PHE A 575 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ILE A 540 " --> pdb=" O PHE A 575 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 26 through 27 Processing sheet with id=AA7, first strand: chain 'F' and resid 110 through 111 Processing sheet with id=AA8, first strand: chain 'F' and resid 117 through 118 removed outlier: 3.841A pdb=" N LEU F 117 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 268 through 269 removed outlier: 6.306A pdb=" N ALA F 299 " --> pdb=" O ILE F 342 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N MET F 344 " --> pdb=" O ALA F 299 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ILE F 301 " --> pdb=" O MET F 344 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ALA F 346 " --> pdb=" O ILE F 301 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ILE F 303 " --> pdb=" O ALA F 346 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 538 through 542 removed outlier: 6.626A pdb=" N ASN F 538 " --> pdb=" O VAL F 573 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N PHE F 575 " --> pdb=" O ASN F 538 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE F 540 " --> pdb=" O PHE F 575 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N ASP F 577 " --> pdb=" O ILE F 540 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ILE F 542 " --> pdb=" O ASP F 577 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLN F 641 " --> pdb=" O GLY F 513 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 25 through 29 removed outlier: 7.756A pdb=" N ILE E 82 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE E 27 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL E 39 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 151 through 155 removed outlier: 6.720A pdb=" N HIS E 115 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR E 168 " --> pdb=" O ARG E 113 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ARG E 113 " --> pdb=" O THR E 168 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 145 through 147 removed outlier: 3.578A pdb=" N CYS E 174 " --> pdb=" O ILE E 146 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 269 through 270 removed outlier: 6.138A pdb=" N ILE E 301 " --> pdb=" O MET E 344 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N ALA E 346 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ILE E 303 " --> pdb=" O ALA E 346 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR E 347 " --> pdb=" O LEU E 243 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N GLY E 240 " --> pdb=" O ARG E 365 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N VAL E 367 " --> pdb=" O GLY E 240 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LEU E 242 " --> pdb=" O VAL E 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 538 through 541 removed outlier: 6.308A pdb=" N CYS E 572 " --> pdb=" O PHE E 618 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ILE E 620 " --> pdb=" O CYS E 572 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LEU E 574 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA E 622 " --> pdb=" O LEU E 574 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL E 514 " --> pdb=" O GLY E 621 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY E 513 " --> pdb=" O GLN E 641 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N ILE E 643 " --> pdb=" O GLY E 513 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU E 515 " --> pdb=" O ILE E 643 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 81 through 84 removed outlier: 5.531A pdb=" N ILE D 27 " --> pdb=" O ILE D 82 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N MET D 84 " --> pdb=" O ILE D 27 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N ASP D 29 " --> pdb=" O MET D 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 38 through 41 removed outlier: 6.113A pdb=" N VAL D 39 " --> pdb=" O LEU D 72 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AC1, first strand: chain 'D' and resid 109 through 110 removed outlier: 6.303A pdb=" N LYS D 109 " --> pdb=" O ILE D 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'D' and resid 151 through 155 removed outlier: 5.276A pdb=" N VAL D 165 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LEU D 117 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU D 167 " --> pdb=" O HIS D 115 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE D 114 " --> pdb=" O HIS D 183 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 269 through 270 removed outlier: 7.213A pdb=" N ILE D 269 " --> pdb=" O ASP D 304 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA D 299 " --> pdb=" O ILE D 342 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N MET D 344 " --> pdb=" O ALA D 299 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE D 301 " --> pdb=" O MET D 344 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N ALA D 346 " --> pdb=" O ILE D 301 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ILE D 303 " --> pdb=" O ALA D 346 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N ILE D 241 " --> pdb=" O ALA D 345 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N THR D 347 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 243 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 367 " --> pdb=" O LEU D 242 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N TYR D 244 " --> pdb=" O VAL D 367 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 538 through 542 removed outlier: 4.074A pdb=" N ASP D 577 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N CYS D 572 " --> pdb=" O PHE D 618 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE D 620 " --> pdb=" O CYS D 572 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU D 574 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA D 622 " --> pdb=" O LEU D 574 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE D 576 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N GLY D 513 " --> pdb=" O GLN D 641 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ILE D 643 " --> pdb=" O GLY D 513 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 515 " --> pdb=" O ILE D 643 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 25 through 30 removed outlier: 7.963A pdb=" N ILE C 82 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE C 27 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET C 84 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N ASP C 29 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE C 100 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 151 through 155 removed outlier: 3.547A pdb=" N VAL C 161 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL C 165 " --> pdb=" O LEU C 117 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU C 117 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE C 114 " --> pdb=" O HIS C 183 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 145 through 147 removed outlier: 3.551A pdb=" N CYS C 174 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 268 through 270 removed outlier: 6.146A pdb=" N ILE C 301 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ALA C 346 " --> pdb=" O ILE C 301 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE C 303 " --> pdb=" O ALA C 346 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N GLY C 240 " --> pdb=" O ARG C 365 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N VAL C 367 " --> pdb=" O GLY C 240 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU C 242 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 538 through 542 removed outlier: 7.375A pdb=" N ASN C 538 " --> pdb=" O VAL C 573 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N PHE C 575 " --> pdb=" O ASN C 538 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE C 540 " --> pdb=" O PHE C 575 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N ASP C 577 " --> pdb=" O ILE C 540 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N ILE C 542 " --> pdb=" O ASP C 577 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N CYS C 572 " --> pdb=" O PHE C 618 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE C 620 " --> pdb=" O CYS C 572 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU C 574 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ALA C 622 " --> pdb=" O LEU C 574 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N PHE C 576 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N GLY C 513 " --> pdb=" O GLN C 641 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ILE C 643 " --> pdb=" O GLY C 513 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU C 515 " --> pdb=" O ILE C 643 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 25 through 30 removed outlier: 7.669A pdb=" N ILE B 82 " --> pdb=" O ARG B 25 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE B 27 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N MET B 84 " --> pdb=" O ILE B 27 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ASP B 29 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B 39 " --> pdb=" O LEU B 72 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N CYS B 69 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 151 through 156 removed outlier: 5.477A pdb=" N VAL B 165 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU B 117 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL B 116 " --> pdb=" O HIS B 183 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 145 through 147 Processing sheet with id=AD4, first strand: chain 'B' and resid 269 through 270 removed outlier: 3.872A pdb=" N ASP B 304 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA B 345 " --> pdb=" O ILE B 241 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 243 " --> pdb=" O ALA B 345 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR B 347 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 539 through 542 removed outlier: 4.099A pdb=" N ILE B 540 " --> pdb=" O VAL B 573 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE B 575 " --> pdb=" O ILE B 540 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 577 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN B 641 " --> pdb=" O GLY B 513 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR B 517 " --> pdb=" O ILE B 643 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 300 through 301 Processing sheet with id=AD7, first strand: chain 'I' and resid 346 through 347 removed outlier: 4.747A pdb=" N LYS I 346 " --> pdb=" O THR I 341 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR I 341 " --> pdb=" O LYS I 346 " (cutoff:3.500A) 1235 hydrogen bonds defined for protein. 3633 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: 7.81 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10998 1.34 - 1.46: 5221 1.46 - 1.58: 19400 1.58 - 1.70: 36 1.70 - 1.82: 292 Bond restraints: 35947 Sorted by residual: bond pdb=" C PRO F 237 " pdb=" N PRO F 238 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.59e+00 bond pdb=" C PRO C 237 " pdb=" N PRO C 238 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.36e+00 bond pdb=" C SER A 171 " pdb=" N PRO A 172 " ideal model delta sigma weight residual 1.334 1.389 -0.055 2.34e-02 1.83e+03 5.53e+00 bond pdb=" C PRO E 237 " pdb=" N PRO E 238 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.21e+00 bond pdb=" CB ASP B 669 " pdb=" CG ASP B 669 " ideal model delta sigma weight residual 1.516 1.572 -0.056 2.50e-02 1.60e+03 4.99e+00 ... (remaining 35942 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.75: 47901 3.75 - 7.49: 600 7.49 - 11.24: 82 11.24 - 14.98: 8 14.98 - 18.73: 2 Bond angle restraints: 48593 Sorted by residual: angle pdb=" N VAL A 399 " pdb=" CA VAL A 399 " pdb=" C VAL A 399 " ideal model delta sigma weight residual 112.96 107.15 5.81 1.00e+00 1.00e+00 3.37e+01 angle pdb=" N GLU A 261 " pdb=" CA GLU A 261 " pdb=" C GLU A 261 " ideal model delta sigma weight residual 114.56 107.21 7.35 1.27e+00 6.20e-01 3.35e+01 angle pdb=" CA LEU F 548 " pdb=" CB LEU F 548 " pdb=" CG LEU F 548 " ideal model delta sigma weight residual 116.30 135.03 -18.73 3.50e+00 8.16e-02 2.86e+01 angle pdb=" C LYS D 614 " pdb=" N LYS D 615 " pdb=" CA LYS D 615 " ideal model delta sigma weight residual 121.54 131.76 -10.22 1.91e+00 2.74e-01 2.86e+01 angle pdb=" C LYS B 63 " pdb=" N ARG B 64 " pdb=" CA ARG B 64 " ideal model delta sigma weight residual 122.08 129.90 -7.82 1.47e+00 4.63e-01 2.83e+01 ... (remaining 48588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 21736 35.20 - 70.41: 496 70.41 - 105.61: 35 105.61 - 140.81: 11 140.81 - 176.01: 3 Dihedral angle restraints: 22281 sinusoidal: 9388 harmonic: 12893 Sorted by residual: dihedral pdb=" CA ARG B 22 " pdb=" C ARG B 22 " pdb=" N PRO B 23 " pdb=" CA PRO B 23 " ideal model delta harmonic sigma weight residual 180.00 -134.13 -45.87 0 5.00e+00 4.00e-02 8.41e+01 dihedral pdb=" CA PHE I 343 " pdb=" C PHE I 343 " pdb=" N PRO I 344 " pdb=" CA PRO I 344 " ideal model delta harmonic sigma weight residual 180.00 135.03 44.97 0 5.00e+00 4.00e-02 8.09e+01 dihedral pdb=" CA ILE A 114 " pdb=" C ILE A 114 " pdb=" N HIS A 115 " pdb=" CA HIS A 115 " ideal model delta harmonic sigma weight residual 180.00 -139.48 -40.52 0 5.00e+00 4.00e-02 6.57e+01 ... (remaining 22278 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4698 0.087 - 0.174: 713 0.174 - 0.260: 50 0.260 - 0.347: 5 0.347 - 0.434: 4 Chirality restraints: 5470 Sorted by residual: chirality pdb=" CB VAL D 407 " pdb=" CA VAL D 407 " pdb=" CG1 VAL D 407 " pdb=" CG2 VAL D 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CB VAL A 407 " pdb=" CA VAL A 407 " pdb=" CG1 VAL A 407 " pdb=" CG2 VAL A 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CB VAL F 407 " pdb=" CA VAL F 407 " pdb=" CG1 VAL F 407 " pdb=" CG2 VAL F 407 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.65e+00 ... (remaining 5467 not shown) Planarity restraints: 6370 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 22 " 0.021 2.00e-02 2.50e+03 4.13e-02 1.71e+01 pdb=" C ARG B 22 " -0.071 2.00e-02 2.50e+03 pdb=" O ARG B 22 " 0.027 2.00e-02 2.50e+03 pdb=" N PRO B 23 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 169 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO D 170 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO D 170 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 170 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 271 " -0.060 5.00e-02 4.00e+02 9.01e-02 1.30e+01 pdb=" N PRO B 272 " 0.156 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.049 5.00e-02 4.00e+02 ... (remaining 6367 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9517 2.81 - 3.33: 32260 3.33 - 3.85: 59487 3.85 - 4.38: 66509 4.38 - 4.90: 108528 Nonbonded interactions: 276301 Sorted by model distance: nonbonded pdb=" O CYS D 522 " pdb=" OG1 THR D 525 " model vdw 2.286 3.040 nonbonded pdb=" O PRO D 272 " pdb=" OG SER D 276 " model vdw 2.295 3.040 nonbonded pdb=" OG1 THR C 448 " pdb=" OD1 ASP C 450 " model vdw 2.302 3.040 nonbonded pdb=" OG SER D 702 " pdb=" O PRO D 727 " model vdw 2.323 3.040 nonbonded pdb=" O LEU B 381 " pdb=" OG1 THR B 385 " model vdw 2.325 3.040 ... (remaining 276296 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' and (resid 24 through 168 or (resid 169 and (name N or name CA or nam \ e C or name O or name CB )) or resid 170 through 432 or resid 439 through 587 or \ resid 598 through 763 or resid 901 through 902)) selection = (chain 'B' and (resid 24 through 94 or (resid 95 and (name N or name CA or name \ C or name O )) or resid 96 through 587 or resid 598 through 763 or resid 901 thr \ ough 902)) selection = (chain 'C' and (resid 24 through 94 or (resid 95 and (name N or name CA or name \ C or name O )) or resid 96 through 587 or resid 598 through 763 or resid 901 thr \ ough 902)) selection = (chain 'D' and (resid 24 through 94 or (resid 95 and (name N or name CA or name \ C or name O )) or resid 96 through 432 or resid 439 through 587 or resid 598 thr \ ough 763 or resid 901 through 902)) selection = (chain 'E' and (resid 24 through 94 or (resid 95 and (name N or name CA or name \ C or name O )) or resid 96 through 432 or resid 439 through 587 or resid 598 thr \ ough 763 or resid 901 through 902)) selection = (chain 'F' and (resid 24 through 168 or (resid 169 and (name N or name CA or nam \ e C or name O or name CB )) or resid 170 through 763 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.630 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 30.580 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 35947 Z= 0.215 Angle : 1.024 18.726 48593 Z= 0.537 Chirality : 0.059 0.434 5470 Planarity : 0.008 0.101 6370 Dihedral : 15.884 176.014 13901 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.07 % 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 are not related in a simple way. whole: -3.13 (0.11), residues: 4424 helix: -2.17 (0.10), residues: 1687 sheet: -0.69 (0.22), residues: 550 loop : -2.36 (0.12), residues: 2187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 313 TYR 0.014 0.002 TYR A 134 PHE 0.037 0.002 PHE C 363 TRP 0.013 0.001 TRP B 454 HIS 0.008 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00421 (35947) covalent geometry : angle 1.02398 (48593) hydrogen bonds : bond 0.17599 ( 1235) hydrogen bonds : angle 7.83043 ( 3633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 932 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 932 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.8974 (pm20) cc_final: 0.8693 (mp0) REVERT: A 218 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8199 (tt0) REVERT: A 241 ILE cc_start: 0.9442 (mm) cc_final: 0.9081 (tp) REVERT: A 274 ILE cc_start: 0.9597 (mm) cc_final: 0.9328 (tp) REVERT: A 300 ILE cc_start: 0.9585 (mt) cc_final: 0.9320 (tp) REVERT: A 360 PHE cc_start: 0.7711 (m-10) cc_final: 0.5522 (m-80) REVERT: A 365 ARG cc_start: 0.9339 (tpt90) cc_final: 0.8751 (mmm160) REVERT: A 388 MET cc_start: 0.7763 (ppp) cc_final: 0.7214 (ppp) REVERT: A 562 ILE cc_start: 0.9676 (mm) cc_final: 0.9383 (mt) REVERT: A 565 LYS cc_start: 0.8882 (pttt) cc_final: 0.8088 (pttm) REVERT: A 567 ARG cc_start: 0.9021 (mmm160) cc_final: 0.8201 (ttp80) REVERT: A 603 GLN cc_start: 0.9577 (mm-40) cc_final: 0.9190 (mm-40) REVERT: A 607 GLU cc_start: 0.9170 (mm-30) cc_final: 0.7867 (mm-30) REVERT: A 700 ARG cc_start: 0.8278 (ptm160) cc_final: 0.7943 (tmt170) REVERT: A 757 MET cc_start: 0.8598 (mtp) cc_final: 0.8273 (mmp) REVERT: F 55 ASP cc_start: 0.8555 (m-30) cc_final: 0.8354 (t0) REVERT: F 220 VAL cc_start: 0.9177 (t) cc_final: 0.8864 (m) REVERT: F 304 ASP cc_start: 0.8872 (t0) cc_final: 0.8609 (t0) REVERT: F 305 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8376 (mm-30) REVERT: F 352 SER cc_start: 0.9466 (t) cc_final: 0.9233 (p) REVERT: F 368 ASP cc_start: 0.8996 (p0) cc_final: 0.8773 (t0) REVERT: F 369 ILE cc_start: 0.9667 (mm) cc_final: 0.9402 (tp) REVERT: F 381 LEU cc_start: 0.9613 (tp) cc_final: 0.9343 (tp) REVERT: F 420 LEU cc_start: 0.9428 (tp) cc_final: 0.8641 (tp) REVERT: F 423 ILE cc_start: 0.9280 (mt) cc_final: 0.9019 (mt) REVERT: F 440 GLU cc_start: 0.7886 (mp0) cc_final: 0.7433 (tm-30) REVERT: F 449 MET cc_start: 0.8450 (pmm) cc_final: 0.7854 (ppp) REVERT: F 450 ASP cc_start: 0.8616 (t70) cc_final: 0.8401 (p0) REVERT: F 478 ASP cc_start: 0.8556 (p0) cc_final: 0.7901 (t70) REVERT: F 498 GLU cc_start: 0.8965 (tt0) cc_final: 0.8765 (mp0) REVERT: F 508 MET cc_start: 0.6334 (ttm) cc_final: 0.5266 (ttm) REVERT: F 541 SER cc_start: 0.9122 (p) cc_final: 0.8809 (t) REVERT: F 551 TRP cc_start: 0.7767 (t60) cc_final: 0.7396 (t60) REVERT: F 599 ARG cc_start: 0.9088 (mtt180) cc_final: 0.8667 (ttm110) REVERT: F 639 LEU cc_start: 0.8364 (mp) cc_final: 0.7930 (tt) REVERT: F 642 LEU cc_start: 0.8236 (mt) cc_final: 0.8019 (mt) REVERT: F 765 ARG cc_start: 0.8279 (tpp80) cc_final: 0.7697 (tmm160) REVERT: E 164 LYS cc_start: 0.7981 (tttp) cc_final: 0.7646 (mtmt) REVERT: E 253 LEU cc_start: 0.9244 (mp) cc_final: 0.8891 (mp) REVERT: E 273 GLU cc_start: 0.8991 (mp0) cc_final: 0.8237 (tm-30) REVERT: E 291 GLU cc_start: 0.8978 (mp0) cc_final: 0.8605 (mp0) REVERT: E 309 ILE cc_start: 0.9568 (mt) cc_final: 0.9303 (mp) REVERT: E 344 MET cc_start: 0.9395 (mtt) cc_final: 0.8918 (mtt) REVERT: E 462 SER cc_start: 0.8245 (p) cc_final: 0.8011 (t) REVERT: E 468 VAL cc_start: 0.8926 (m) cc_final: 0.8652 (p) REVERT: E 540 ILE cc_start: 0.9001 (mt) cc_final: 0.8795 (mm) REVERT: E 542 ILE cc_start: 0.9529 (mm) cc_final: 0.9307 (mp) REVERT: E 543 LYS cc_start: 0.9140 (mmpt) cc_final: 0.8912 (mmtm) REVERT: E 563 PHE cc_start: 0.9378 (m-80) cc_final: 0.9140 (m-80) REVERT: E 584 LYS cc_start: 0.8476 (tmtt) cc_final: 0.8193 (mttm) REVERT: E 607 GLU cc_start: 0.9561 (mm-30) cc_final: 0.8946 (mm-30) REVERT: E 678 MET cc_start: 0.9124 (mpp) cc_final: 0.8647 (mpp) REVERT: D 241 ILE cc_start: 0.9111 (mp) cc_final: 0.8886 (mm) REVERT: D 244 TYR cc_start: 0.7928 (p90) cc_final: 0.7238 (p90) REVERT: D 329 LEU cc_start: 0.9417 (mt) cc_final: 0.9157 (mt) REVERT: D 357 LEU cc_start: 0.9415 (tp) cc_final: 0.8881 (tp) REVERT: D 360 PHE cc_start: 0.8644 (m-80) cc_final: 0.8318 (m-10) REVERT: D 388 MET cc_start: 0.8971 (ppp) cc_final: 0.8722 (ppp) REVERT: D 415 CYS cc_start: 0.9443 (m) cc_final: 0.9128 (p) REVERT: D 417 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8698 (tm-30) REVERT: D 464 LEU cc_start: 0.8951 (tp) cc_final: 0.8588 (tp) REVERT: D 515 LEU cc_start: 0.9521 (tp) cc_final: 0.9297 (tp) REVERT: D 542 ILE cc_start: 0.9613 (mm) cc_final: 0.9346 (mp) REVERT: D 560 ARG cc_start: 0.8197 (mtt-85) cc_final: 0.7946 (mmm-85) REVERT: D 574 LEU cc_start: 0.9647 (mm) cc_final: 0.9440 (mm) REVERT: C 84 MET cc_start: 0.6112 (ptp) cc_final: 0.5587 (ppp) REVERT: C 275 MET cc_start: 0.9459 (mmm) cc_final: 0.9251 (mmm) REVERT: C 305 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8820 (mm-30) REVERT: C 336 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8534 (mmtm) REVERT: C 449 MET cc_start: 0.8782 (ttm) cc_final: 0.8197 (mtp) REVERT: C 560 ARG cc_start: 0.9205 (mtp180) cc_final: 0.8896 (mtp85) REVERT: C 607 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8415 (mt-10) REVERT: C 623 THR cc_start: 0.9320 (m) cc_final: 0.9091 (m) REVERT: C 662 ARG cc_start: 0.9523 (mpt180) cc_final: 0.9247 (mpp-170) REVERT: C 689 GLU cc_start: 0.9150 (tt0) cc_final: 0.8787 (mt-10) REVERT: C 740 MET cc_start: 0.8530 (ptt) cc_final: 0.8291 (ptt) REVERT: C 756 GLU cc_start: 0.9387 (mp0) cc_final: 0.9158 (tm-30) REVERT: B 138 TYR cc_start: 0.3554 (t80) cc_final: 0.3017 (t80) REVERT: B 246 PRO cc_start: 0.8943 (Cg_exo) cc_final: 0.8640 (Cg_endo) REVERT: B 375 THR cc_start: 0.9028 (p) cc_final: 0.8717 (t) REVERT: B 379 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9087 (mm-30) REVERT: B 407 VAL cc_start: 0.9196 (t) cc_final: 0.8930 (p) REVERT: B 417 GLU cc_start: 0.9452 (tp30) cc_final: 0.8936 (tm-30) REVERT: B 465 ARG cc_start: 0.8874 (ptt-90) cc_final: 0.8016 (ptt-90) REVERT: B 565 LYS cc_start: 0.9267 (ttmm) cc_final: 0.8422 (tppt) REVERT: B 611 MET cc_start: 0.7448 (tpt) cc_final: 0.6720 (tpt) REVERT: B 643 ILE cc_start: 0.9335 (mm) cc_final: 0.8702 (mt) outliers start: 0 outliers final: 0 residues processed: 932 average time/residue: 0.2549 time to fit residues: 367.7315 Evaluate side-chains 574 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 574 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 432 optimal weight: 5.9990 chunk 197 optimal weight: 0.3980 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 1.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** F 616 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 660 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN E 558 ASN D 384 HIS ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 602 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.114111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.079573 restraints weight = 138625.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.081716 restraints weight = 95386.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.083334 restraints weight = 73472.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.084405 restraints weight = 60413.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.085180 restraints weight = 51919.988| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35947 Z= 0.157 Angle : 0.738 12.623 48593 Z= 0.365 Chirality : 0.047 0.192 5470 Planarity : 0.006 0.070 6370 Dihedral : 10.225 170.630 4987 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.13 % Allowed : 4.99 % Favored : 94.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.02 % 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 are not related in a simple way. whole: -2.11 (0.12), residues: 4424 helix: -0.75 (0.12), residues: 1712 sheet: -0.78 (0.21), residues: 575 loop : -2.12 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 635 TYR 0.021 0.001 TYR A 134 PHE 0.044 0.002 PHE F 563 TRP 0.009 0.001 TRP B 476 HIS 0.006 0.001 HIS C 115 Details of bonding type rmsd covalent geometry : bond 0.00332 (35947) covalent geometry : angle 0.73801 (48593) hydrogen bonds : bond 0.04081 ( 1235) hydrogen bonds : angle 5.84675 ( 3633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 695 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8385 (mp) cc_final: 0.7969 (mt) REVERT: A 200 GLU cc_start: 0.8906 (pm20) cc_final: 0.8661 (mp0) REVERT: A 218 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8035 (tt0) REVERT: A 241 ILE cc_start: 0.9498 (mm) cc_final: 0.9166 (tp) REVERT: A 305 GLU cc_start: 0.8628 (tp30) cc_final: 0.7646 (tp30) REVERT: A 321 GLU cc_start: 0.8926 (mp0) cc_final: 0.8655 (mp0) REVERT: A 388 MET cc_start: 0.7921 (ppp) cc_final: 0.7168 (ppp) REVERT: A 476 TRP cc_start: 0.7921 (t-100) cc_final: 0.7169 (t-100) REVERT: A 517 TYR cc_start: 0.6865 (p90) cc_final: 0.5022 (p90) REVERT: A 560 ARG cc_start: 0.9160 (mmm160) cc_final: 0.8275 (mtt180) REVERT: A 562 ILE cc_start: 0.9686 (mm) cc_final: 0.9483 (mt) REVERT: A 567 ARG cc_start: 0.9099 (mmm160) cc_final: 0.8601 (ttp80) REVERT: A 603 GLN cc_start: 0.9635 (mm-40) cc_final: 0.8520 (mm-40) REVERT: A 607 GLU cc_start: 0.8722 (mm-30) cc_final: 0.7899 (mm-30) REVERT: A 642 LEU cc_start: 0.9327 (mp) cc_final: 0.9007 (tp) REVERT: A 757 MET cc_start: 0.8700 (mtp) cc_final: 0.8387 (mmp) REVERT: F 55 ASP cc_start: 0.8535 (m-30) cc_final: 0.8331 (t70) REVERT: F 218 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7635 (tp30) REVERT: F 220 VAL cc_start: 0.8997 (t) cc_final: 0.8506 (m) REVERT: F 222 LEU cc_start: 0.8777 (mm) cc_final: 0.8179 (mm) REVERT: F 304 ASP cc_start: 0.8860 (t0) cc_final: 0.8449 (t0) REVERT: F 305 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8144 (mm-30) REVERT: F 332 MET cc_start: 0.8757 (tpt) cc_final: 0.8529 (tpt) REVERT: F 369 ILE cc_start: 0.9742 (mm) cc_final: 0.9512 (tp) REVERT: F 440 GLU cc_start: 0.8281 (mp0) cc_final: 0.7900 (tm-30) REVERT: F 449 MET cc_start: 0.8619 (pmm) cc_final: 0.8326 (ppp) REVERT: F 450 ASP cc_start: 0.8352 (t70) cc_final: 0.7828 (t0) REVERT: F 478 ASP cc_start: 0.8386 (p0) cc_final: 0.8018 (t70) REVERT: F 498 GLU cc_start: 0.9025 (tt0) cc_final: 0.8760 (mt-10) REVERT: F 541 SER cc_start: 0.9011 (p) cc_final: 0.8802 (t) REVERT: F 551 TRP cc_start: 0.7777 (t60) cc_final: 0.7091 (t60) REVERT: F 599 ARG cc_start: 0.8973 (mtt180) cc_final: 0.8540 (ttm110) REVERT: F 639 LEU cc_start: 0.8671 (mp) cc_final: 0.8399 (tt) REVERT: F 642 LEU cc_start: 0.8126 (mt) cc_final: 0.7900 (mt) REVERT: F 765 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7709 (tmm160) REVERT: E 243 LEU cc_start: 0.8889 (mp) cc_final: 0.8678 (mp) REVERT: E 273 GLU cc_start: 0.8910 (mp0) cc_final: 0.8390 (tm-30) REVERT: E 414 LEU cc_start: 0.9661 (mt) cc_final: 0.9263 (mt) REVERT: E 546 GLU cc_start: 0.9560 (tp30) cc_final: 0.9354 (tp30) REVERT: E 563 PHE cc_start: 0.9314 (m-80) cc_final: 0.8995 (m-80) REVERT: E 565 LYS cc_start: 0.9425 (mttp) cc_final: 0.9196 (mttt) REVERT: E 584 LYS cc_start: 0.8625 (tmtt) cc_final: 0.8279 (mttm) REVERT: E 615 LYS cc_start: 0.9153 (mmtt) cc_final: 0.8944 (mmtp) REVERT: E 678 MET cc_start: 0.8996 (mpp) cc_final: 0.8607 (mpp) REVERT: E 757 MET cc_start: 0.9383 (ptt) cc_final: 0.9153 (ppp) REVERT: D 205 ASP cc_start: 0.8779 (t0) cc_final: 0.8575 (t0) REVERT: D 244 TYR cc_start: 0.8105 (p90) cc_final: 0.7406 (p90) REVERT: D 292 GLU cc_start: 0.8607 (tm-30) cc_final: 0.8384 (tm-30) REVERT: D 305 GLU cc_start: 0.9197 (tp30) cc_final: 0.8920 (tp30) REVERT: D 343 VAL cc_start: 0.9446 (t) cc_final: 0.9214 (p) REVERT: D 344 MET cc_start: 0.8837 (tpt) cc_final: 0.8349 (tpp) REVERT: D 360 PHE cc_start: 0.8471 (m-80) cc_final: 0.8260 (m-10) REVERT: D 402 GLU cc_start: 0.8792 (mp0) cc_final: 0.8556 (pp20) REVERT: D 415 CYS cc_start: 0.9450 (m) cc_final: 0.9164 (p) REVERT: D 417 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8713 (tm-30) REVERT: D 563 PHE cc_start: 0.8669 (m-80) cc_final: 0.8314 (m-10) REVERT: D 574 LEU cc_start: 0.9334 (mm) cc_final: 0.9038 (mm) REVERT: D 608 MET cc_start: 0.9459 (ttp) cc_final: 0.9164 (ttp) REVERT: D 620 ILE cc_start: 0.9291 (mp) cc_final: 0.9091 (tp) REVERT: C 84 MET cc_start: 0.5629 (ptp) cc_final: 0.5355 (ppp) REVERT: C 305 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8799 (mm-30) REVERT: C 449 MET cc_start: 0.8540 (ttm) cc_final: 0.8130 (mtp) REVERT: C 561 GLU cc_start: 0.9070 (mp0) cc_final: 0.8869 (mp0) REVERT: C 607 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8237 (mt-10) REVERT: C 680 ASN cc_start: 0.8909 (p0) cc_final: 0.8706 (p0) REVERT: C 689 GLU cc_start: 0.9170 (tt0) cc_final: 0.8829 (mt-10) REVERT: C 740 MET cc_start: 0.8718 (ptt) cc_final: 0.8504 (ptt) REVERT: B 138 TYR cc_start: 0.3153 (t80) cc_final: 0.2577 (t80) REVERT: B 246 PRO cc_start: 0.9229 (Cg_exo) cc_final: 0.8980 (Cg_endo) REVERT: B 266 PHE cc_start: 0.8868 (p90) cc_final: 0.8395 (p90) REVERT: B 275 MET cc_start: 0.9120 (mtp) cc_final: 0.8591 (mtp) REVERT: B 301 ILE cc_start: 0.9271 (tp) cc_final: 0.9028 (tt) REVERT: B 375 THR cc_start: 0.9087 (p) cc_final: 0.8818 (t) REVERT: B 379 GLU cc_start: 0.9389 (mt-10) cc_final: 0.9080 (mm-30) REVERT: B 417 GLU cc_start: 0.9458 (tp30) cc_final: 0.9070 (tm-30) REVERT: B 452 PHE cc_start: 0.9031 (m-80) cc_final: 0.8619 (m-80) REVERT: B 454 TRP cc_start: 0.8665 (t60) cc_final: 0.8430 (t-100) REVERT: B 517 TYR cc_start: 0.8609 (p90) cc_final: 0.8290 (p90) REVERT: B 565 LYS cc_start: 0.9183 (ttmm) cc_final: 0.8424 (tppt) REVERT: B 568 GLN cc_start: 0.9356 (tp-100) cc_final: 0.9036 (tp-100) REVERT: B 609 ASP cc_start: 0.8305 (m-30) cc_final: 0.7438 (m-30) REVERT: B 611 MET cc_start: 0.6758 (tpt) cc_final: 0.5030 (tpt) REVERT: B 620 ILE cc_start: 0.9764 (mt) cc_final: 0.9379 (tt) REVERT: B 678 MET cc_start: 0.7425 (mtt) cc_final: 0.6912 (mtt) REVERT: B 753 ARG cc_start: 0.9364 (ppt170) cc_final: 0.8986 (ttp80) REVERT: B 757 MET cc_start: 0.9260 (tmm) cc_final: 0.8978 (tmm) outliers start: 5 outliers final: 3 residues processed: 700 average time/residue: 0.2267 time to fit residues: 252.5480 Evaluate side-chains 525 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 522 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 126 optimal weight: 10.0000 chunk 265 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 438 optimal weight: 50.0000 chunk 288 optimal weight: 40.0000 chunk 426 optimal weight: 0.1980 chunk 68 optimal weight: 0.8980 chunk 364 optimal weight: 30.0000 chunk 131 optimal weight: 0.7980 chunk 369 optimal weight: 6.9990 chunk 273 optimal weight: 0.7980 overall best weight: 1.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS F 616 ASN F 660 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN E 558 ASN E 568 GLN D 260 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 327 GLN D 404 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS B 458 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.114337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079782 restraints weight = 136891.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.082140 restraints weight = 93866.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.083671 restraints weight = 70426.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.084903 restraints weight = 57828.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.085603 restraints weight = 49053.021| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35947 Z= 0.140 Angle : 0.720 11.381 48593 Z= 0.351 Chirality : 0.047 0.179 5470 Planarity : 0.006 0.114 6370 Dihedral : 10.039 162.437 4987 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 0.11 % Allowed : 4.09 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.02 % 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 are not related in a simple way. whole: -1.79 (0.12), residues: 4424 helix: -0.31 (0.12), residues: 1714 sheet: -0.78 (0.21), residues: 591 loop : -2.07 (0.13), residues: 2119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG F 635 TYR 0.018 0.001 TYR A 134 PHE 0.021 0.001 PHE C 363 TRP 0.019 0.002 TRP B 476 HIS 0.007 0.001 HIS F 735 Details of bonding type rmsd covalent geometry : bond 0.00305 (35947) covalent geometry : angle 0.71989 (48593) hydrogen bonds : bond 0.03708 ( 1235) hydrogen bonds : angle 5.61645 ( 3633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 655 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 135 LEU cc_start: 0.8457 (mp) cc_final: 0.8112 (mt) REVERT: A 200 GLU cc_start: 0.8922 (pm20) cc_final: 0.8700 (mp0) REVERT: A 218 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7814 (tt0) REVERT: A 241 ILE cc_start: 0.9418 (mm) cc_final: 0.9076 (tp) REVERT: A 305 GLU cc_start: 0.8248 (tp30) cc_final: 0.7376 (tp30) REVERT: A 321 GLU cc_start: 0.8999 (mp0) cc_final: 0.8691 (mp0) REVERT: A 388 MET cc_start: 0.7978 (ppp) cc_final: 0.7205 (ppp) REVERT: A 476 TRP cc_start: 0.7961 (t-100) cc_final: 0.7206 (t-100) REVERT: A 560 ARG cc_start: 0.9169 (mmm160) cc_final: 0.8341 (mtt180) REVERT: A 562 ILE cc_start: 0.9633 (mm) cc_final: 0.9411 (mt) REVERT: A 567 ARG cc_start: 0.9107 (mmm160) cc_final: 0.8697 (ttp-170) REVERT: A 603 GLN cc_start: 0.9701 (mm-40) cc_final: 0.8577 (mm-40) REVERT: A 607 GLU cc_start: 0.8803 (mm-30) cc_final: 0.7635 (mm-30) REVERT: A 757 MET cc_start: 0.8702 (mtp) cc_final: 0.8422 (mmp) REVERT: F 55 ASP cc_start: 0.8651 (m-30) cc_final: 0.8373 (t70) REVERT: F 218 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7521 (tp30) REVERT: F 220 VAL cc_start: 0.8933 (t) cc_final: 0.8390 (m) REVERT: F 222 LEU cc_start: 0.8705 (mm) cc_final: 0.8025 (mm) REVERT: F 304 ASP cc_start: 0.8745 (t0) cc_final: 0.8443 (t0) REVERT: F 305 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8054 (mm-30) REVERT: F 332 MET cc_start: 0.8823 (tpt) cc_final: 0.8570 (tpt) REVERT: F 337 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8299 (tm-30) REVERT: F 347 THR cc_start: 0.8630 (t) cc_final: 0.8367 (t) REVERT: F 381 LEU cc_start: 0.9718 (mt) cc_final: 0.9491 (pp) REVERT: F 440 GLU cc_start: 0.8484 (mp0) cc_final: 0.8279 (tm-30) REVERT: F 442 MET cc_start: 0.7681 (mtm) cc_final: 0.7255 (tmm) REVERT: F 449 MET cc_start: 0.8587 (pmm) cc_final: 0.8383 (ppp) REVERT: F 450 ASP cc_start: 0.8313 (t70) cc_final: 0.7815 (t0) REVERT: F 478 ASP cc_start: 0.8413 (p0) cc_final: 0.7988 (t70) REVERT: F 498 GLU cc_start: 0.8979 (tt0) cc_final: 0.8637 (mt-10) REVERT: F 599 ARG cc_start: 0.8890 (mtt180) cc_final: 0.8432 (ttm110) REVERT: F 635 ARG cc_start: 0.9044 (mpp-170) cc_final: 0.8772 (mtm-85) REVERT: F 765 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7695 (tmm160) REVERT: E 273 GLU cc_start: 0.8984 (mp0) cc_final: 0.8619 (tm-30) REVERT: E 410 ASP cc_start: 0.8902 (t0) cc_final: 0.8501 (t0) REVERT: E 414 LEU cc_start: 0.9652 (mt) cc_final: 0.9263 (mt) REVERT: E 462 SER cc_start: 0.9031 (t) cc_final: 0.8226 (t) REVERT: E 466 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8728 (mt-10) REVERT: E 546 GLU cc_start: 0.9563 (tp30) cc_final: 0.9305 (tp30) REVERT: E 563 PHE cc_start: 0.9319 (m-80) cc_final: 0.8984 (m-80) REVERT: E 663 LYS cc_start: 0.9135 (ptpp) cc_final: 0.8873 (ptmm) REVERT: E 678 MET cc_start: 0.9105 (mpp) cc_final: 0.8412 (mpp) REVERT: E 757 MET cc_start: 0.9386 (ptt) cc_final: 0.9057 (ppp) REVERT: D 219 MET cc_start: 0.8552 (mmp) cc_final: 0.8205 (mmm) REVERT: D 244 TYR cc_start: 0.8244 (p90) cc_final: 0.7462 (p90) REVERT: D 305 GLU cc_start: 0.9190 (tp30) cc_final: 0.8932 (tp30) REVERT: D 312 LYS cc_start: 0.9417 (mttt) cc_final: 0.8933 (mmmm) REVERT: D 329 LEU cc_start: 0.9389 (mt) cc_final: 0.9186 (mt) REVERT: D 343 VAL cc_start: 0.9421 (t) cc_final: 0.9185 (p) REVERT: D 344 MET cc_start: 0.8873 (tpt) cc_final: 0.8596 (tpp) REVERT: D 360 PHE cc_start: 0.8498 (m-80) cc_final: 0.8283 (m-10) REVERT: D 415 CYS cc_start: 0.9460 (m) cc_final: 0.9182 (p) REVERT: D 417 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8755 (tm-30) REVERT: D 563 PHE cc_start: 0.8576 (m-80) cc_final: 0.8333 (m-10) REVERT: D 598 ASP cc_start: 0.8914 (m-30) cc_final: 0.8479 (m-30) REVERT: D 608 MET cc_start: 0.9440 (ttp) cc_final: 0.8841 (ttp) REVERT: D 609 ASP cc_start: 0.8635 (m-30) cc_final: 0.8352 (m-30) REVERT: C 84 MET cc_start: 0.5616 (ptp) cc_final: 0.5342 (ppp) REVERT: C 242 LEU cc_start: 0.9648 (mp) cc_final: 0.9286 (mp) REVERT: C 305 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8753 (mm-30) REVERT: C 449 MET cc_start: 0.8459 (ttm) cc_final: 0.8145 (mtp) REVERT: C 607 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8258 (mt-10) REVERT: C 689 GLU cc_start: 0.9174 (tt0) cc_final: 0.8861 (mt-10) REVERT: C 736 PHE cc_start: 0.8350 (m-80) cc_final: 0.8086 (m-80) REVERT: C 740 MET cc_start: 0.8767 (ptt) cc_final: 0.8505 (ptt) REVERT: B 110 TYR cc_start: 0.7251 (m-10) cc_final: 0.6821 (m-80) REVERT: B 138 TYR cc_start: 0.3122 (t80) cc_final: 0.2753 (t80) REVERT: B 246 PRO cc_start: 0.9297 (Cg_exo) cc_final: 0.9023 (Cg_endo) REVERT: B 266 PHE cc_start: 0.8904 (p90) cc_final: 0.8414 (p90) REVERT: B 274 ILE cc_start: 0.9501 (tp) cc_final: 0.9202 (tp) REVERT: B 305 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 368 ASP cc_start: 0.8750 (p0) cc_final: 0.8545 (p0) REVERT: B 375 THR cc_start: 0.9118 (p) cc_final: 0.8889 (t) REVERT: B 379 GLU cc_start: 0.9457 (mt-10) cc_final: 0.9219 (mm-30) REVERT: B 410 ASP cc_start: 0.9257 (m-30) cc_final: 0.9008 (m-30) REVERT: B 417 GLU cc_start: 0.9445 (tp30) cc_final: 0.9045 (tm-30) REVERT: B 452 PHE cc_start: 0.9049 (m-80) cc_final: 0.8644 (m-10) REVERT: B 517 TYR cc_start: 0.8632 (p90) cc_final: 0.8308 (p90) REVERT: B 565 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8408 (tppt) REVERT: B 568 GLN cc_start: 0.9300 (tp-100) cc_final: 0.9064 (tp-100) REVERT: B 609 ASP cc_start: 0.8429 (m-30) cc_final: 0.7796 (m-30) REVERT: B 620 ILE cc_start: 0.9740 (mt) cc_final: 0.9362 (tt) REVERT: B 678 MET cc_start: 0.7553 (mtt) cc_final: 0.7047 (mtt) REVERT: B 753 ARG cc_start: 0.9310 (ppt170) cc_final: 0.8902 (ttp80) REVERT: B 757 MET cc_start: 0.9228 (tmm) cc_final: 0.8897 (tmm) outliers start: 4 outliers final: 3 residues processed: 658 average time/residue: 0.2253 time to fit residues: 239.6644 Evaluate side-chains 520 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 517 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 252 optimal weight: 0.1980 chunk 149 optimal weight: 0.9990 chunk 199 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 422 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 302 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 324 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 229 optimal weight: 5.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 384 HIS ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN E 568 GLN D 260 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 735 HIS ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 558 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.113554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.078859 restraints weight = 141126.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.081166 restraints weight = 96844.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.082364 restraints weight = 73439.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.083806 restraints weight = 61340.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.084372 restraints weight = 52179.627| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 35947 Z= 0.138 Angle : 0.717 11.633 48593 Z= 0.348 Chirality : 0.047 0.212 5470 Planarity : 0.005 0.103 6370 Dihedral : 9.912 160.904 4987 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.05 % Allowed : 3.43 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % 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 are not related in a simple way. whole: -1.64 (0.12), residues: 4424 helix: -0.13 (0.12), residues: 1730 sheet: -0.80 (0.21), residues: 592 loop : -2.01 (0.13), residues: 2102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG F 635 TYR 0.018 0.001 TYR C 244 PHE 0.016 0.001 PHE E 736 TRP 0.009 0.001 TRP B 476 HIS 0.004 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00302 (35947) covalent geometry : angle 0.71708 (48593) hydrogen bonds : bond 0.03475 ( 1235) hydrogen bonds : angle 5.43018 ( 3633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 640 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8636 (ttp) cc_final: 0.8395 (ppp) REVERT: A 200 GLU cc_start: 0.8936 (pm20) cc_final: 0.8693 (mp0) REVERT: A 218 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7750 (tt0) REVERT: A 241 ILE cc_start: 0.9392 (mm) cc_final: 0.9026 (tp) REVERT: A 274 ILE cc_start: 0.9784 (mt) cc_final: 0.9472 (tp) REVERT: A 305 GLU cc_start: 0.8229 (tp30) cc_final: 0.7403 (tp30) REVERT: A 321 GLU cc_start: 0.9069 (mp0) cc_final: 0.8721 (mp0) REVERT: A 344 MET cc_start: 0.9042 (mmt) cc_final: 0.8369 (mmt) REVERT: A 388 MET cc_start: 0.8016 (ppp) cc_final: 0.7602 (ppp) REVERT: A 560 ARG cc_start: 0.9193 (mmm160) cc_final: 0.8516 (mmm-85) REVERT: A 562 ILE cc_start: 0.9722 (mm) cc_final: 0.9490 (mt) REVERT: A 567 ARG cc_start: 0.9188 (mmm160) cc_final: 0.8693 (ttp-170) REVERT: A 603 GLN cc_start: 0.9664 (mm-40) cc_final: 0.8574 (mm-40) REVERT: A 607 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8033 (mm-30) REVERT: A 757 MET cc_start: 0.8670 (mtp) cc_final: 0.8401 (mmp) REVERT: F 55 ASP cc_start: 0.8708 (m-30) cc_final: 0.8430 (t70) REVERT: F 218 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7501 (tp30) REVERT: F 222 LEU cc_start: 0.8747 (mm) cc_final: 0.8118 (mm) REVERT: F 304 ASP cc_start: 0.8709 (t0) cc_final: 0.8443 (t0) REVERT: F 305 GLU cc_start: 0.8762 (mt-10) cc_final: 0.7964 (mm-30) REVERT: F 332 MET cc_start: 0.8848 (tpt) cc_final: 0.8616 (tpt) REVERT: F 337 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8237 (tm-30) REVERT: F 442 MET cc_start: 0.7669 (mtm) cc_final: 0.7309 (tmm) REVERT: F 450 ASP cc_start: 0.8256 (t70) cc_final: 0.7750 (t0) REVERT: F 478 ASP cc_start: 0.8374 (p0) cc_final: 0.8045 (t70) REVERT: F 498 GLU cc_start: 0.8977 (tt0) cc_final: 0.8662 (mt-10) REVERT: F 765 ARG cc_start: 0.8244 (tpp80) cc_final: 0.7683 (tmm160) REVERT: E 206 ILE cc_start: 0.9368 (mm) cc_final: 0.9125 (mm) REVERT: E 273 GLU cc_start: 0.8994 (mp0) cc_final: 0.8408 (tm-30) REVERT: E 410 ASP cc_start: 0.8911 (t0) cc_final: 0.8473 (t0) REVERT: E 414 LEU cc_start: 0.9648 (mt) cc_final: 0.9266 (mt) REVERT: E 462 SER cc_start: 0.9063 (t) cc_final: 0.8298 (t) REVERT: E 466 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8682 (mt-10) REVERT: E 546 GLU cc_start: 0.9549 (tp30) cc_final: 0.9318 (tp30) REVERT: E 563 PHE cc_start: 0.9311 (m-80) cc_final: 0.8957 (m-80) REVERT: E 630 ASP cc_start: 0.8959 (p0) cc_final: 0.8575 (p0) REVERT: E 635 ARG cc_start: 0.8892 (ttp-110) cc_final: 0.8685 (ttp-110) REVERT: E 740 MET cc_start: 0.6369 (pmm) cc_final: 0.5843 (pmm) REVERT: E 757 MET cc_start: 0.9290 (ptt) cc_final: 0.9015 (ppp) REVERT: D 219 MET cc_start: 0.8594 (mmp) cc_final: 0.8295 (mmm) REVERT: D 244 TYR cc_start: 0.8462 (p90) cc_final: 0.7358 (p90) REVERT: D 305 GLU cc_start: 0.9121 (tp30) cc_final: 0.8404 (tp30) REVERT: D 329 LEU cc_start: 0.9438 (mt) cc_final: 0.9236 (mt) REVERT: D 343 VAL cc_start: 0.9526 (t) cc_final: 0.9233 (p) REVERT: D 415 CYS cc_start: 0.9459 (m) cc_final: 0.9161 (p) REVERT: D 417 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8719 (tm-30) REVERT: D 563 PHE cc_start: 0.8584 (m-80) cc_final: 0.8233 (m-10) REVERT: D 598 ASP cc_start: 0.8884 (m-30) cc_final: 0.8410 (m-30) REVERT: D 608 MET cc_start: 0.9504 (ttp) cc_final: 0.9110 (ttp) REVERT: D 609 ASP cc_start: 0.8660 (m-30) cc_final: 0.8452 (m-30) REVERT: C 46 MET cc_start: 0.0151 (mtt) cc_final: -0.0236 (mpp) REVERT: C 84 MET cc_start: 0.5765 (ptp) cc_final: 0.5199 (ppp) REVERT: C 305 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8565 (mm-30) REVERT: C 332 MET cc_start: 0.8583 (tmm) cc_final: 0.8378 (tmm) REVERT: C 449 MET cc_start: 0.8415 (ttm) cc_final: 0.8112 (mtp) REVERT: C 607 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8211 (mt-10) REVERT: C 614 LYS cc_start: 0.9272 (mptt) cc_final: 0.8933 (mmtt) REVERT: C 640 ASP cc_start: 0.8208 (p0) cc_final: 0.8007 (t0) REVERT: C 689 GLU cc_start: 0.9160 (tt0) cc_final: 0.8873 (mt-10) REVERT: C 736 PHE cc_start: 0.8348 (m-80) cc_final: 0.8073 (m-80) REVERT: C 740 MET cc_start: 0.8682 (ptt) cc_final: 0.8420 (ptt) REVERT: B 110 TYR cc_start: 0.7262 (m-10) cc_final: 0.6851 (m-80) REVERT: B 138 TYR cc_start: 0.3239 (t80) cc_final: 0.2841 (t80) REVERT: B 246 PRO cc_start: 0.9345 (Cg_exo) cc_final: 0.9120 (Cg_endo) REVERT: B 266 PHE cc_start: 0.8886 (p90) cc_final: 0.8438 (p90) REVERT: B 274 ILE cc_start: 0.9612 (tp) cc_final: 0.9221 (tp) REVERT: B 301 ILE cc_start: 0.9322 (tt) cc_final: 0.9067 (tp) REVERT: B 305 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8428 (tm-30) REVERT: B 375 THR cc_start: 0.9047 (p) cc_final: 0.8813 (t) REVERT: B 379 GLU cc_start: 0.9514 (mt-10) cc_final: 0.9179 (mm-30) REVERT: B 410 ASP cc_start: 0.9240 (m-30) cc_final: 0.8981 (m-30) REVERT: B 417 GLU cc_start: 0.9446 (tp30) cc_final: 0.8900 (tm-30) REVERT: B 452 PHE cc_start: 0.9010 (m-80) cc_final: 0.8622 (m-10) REVERT: B 517 TYR cc_start: 0.8605 (p90) cc_final: 0.8285 (p90) REVERT: B 540 ILE cc_start: 0.9036 (mt) cc_final: 0.8820 (mt) REVERT: B 565 LYS cc_start: 0.9139 (ttmm) cc_final: 0.8457 (tppt) REVERT: B 568 GLN cc_start: 0.9322 (tp-100) cc_final: 0.9080 (tp-100) REVERT: B 607 GLU cc_start: 0.9143 (mp0) cc_final: 0.8938 (pt0) REVERT: B 609 ASP cc_start: 0.8334 (m-30) cc_final: 0.7737 (m-30) REVERT: B 615 LYS cc_start: 0.8337 (mtmm) cc_final: 0.7857 (mtmm) REVERT: B 620 ILE cc_start: 0.9735 (mt) cc_final: 0.9350 (tt) REVERT: B 678 MET cc_start: 0.7806 (mtt) cc_final: 0.7326 (mtt) REVERT: B 753 ARG cc_start: 0.9298 (ppt170) cc_final: 0.8876 (ttp80) REVERT: B 757 MET cc_start: 0.9248 (tmm) cc_final: 0.8905 (tmm) outliers start: 2 outliers final: 0 residues processed: 640 average time/residue: 0.2228 time to fit residues: 229.8723 Evaluate side-chains 508 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 160 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 267 optimal weight: 9.9990 chunk 289 optimal weight: 50.0000 chunk 66 optimal weight: 10.0000 chunk 365 optimal weight: 20.0000 chunk 17 optimal weight: 3.9990 chunk 415 optimal weight: 8.9990 chunk 323 optimal weight: 5.9990 chunk 176 optimal weight: 0.4980 chunk 260 optimal weight: 0.8980 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN F 384 HIS F 533 ASN F 616 ASN E 533 ASN E 538 ASN E 568 GLN D 260 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 458 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.109370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076212 restraints weight = 143567.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.078166 restraints weight = 99220.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079554 restraints weight = 75516.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080665 restraints weight = 61837.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.081371 restraints weight = 53641.221| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 35947 Z= 0.195 Angle : 0.759 12.647 48593 Z= 0.376 Chirality : 0.047 0.231 5470 Planarity : 0.005 0.074 6370 Dihedral : 9.985 159.948 4987 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.05 % Allowed : 3.72 % Favored : 96.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % 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 are not related in a simple way. whole: -1.59 (0.12), residues: 4424 helix: -0.04 (0.12), residues: 1724 sheet: -0.90 (0.21), residues: 588 loop : -1.98 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.001 ARG F 635 TYR 0.024 0.002 TYR C 517 PHE 0.045 0.002 PHE F 563 TRP 0.016 0.002 TRP F 551 HIS 0.006 0.001 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00405 (35947) covalent geometry : angle 0.75906 (48593) hydrogen bonds : bond 0.03694 ( 1235) hydrogen bonds : angle 5.47357 ( 3633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 602 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.8879 (pm20) cc_final: 0.8591 (mp0) REVERT: A 218 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7855 (tt0) REVERT: A 305 GLU cc_start: 0.8270 (tp30) cc_final: 0.7530 (tp30) REVERT: A 321 GLU cc_start: 0.9150 (mp0) cc_final: 0.8832 (mp0) REVERT: A 331 LEU cc_start: 0.9201 (mt) cc_final: 0.8996 (mt) REVERT: A 344 MET cc_start: 0.8981 (mmt) cc_final: 0.8767 (mmp) REVERT: A 388 MET cc_start: 0.8194 (ppp) cc_final: 0.7742 (ppp) REVERT: A 392 ASP cc_start: 0.8555 (t0) cc_final: 0.8308 (t0) REVERT: A 560 ARG cc_start: 0.9099 (mmm160) cc_final: 0.8769 (mmm160) REVERT: A 567 ARG cc_start: 0.9220 (mmm160) cc_final: 0.8892 (ttp-170) REVERT: A 606 THR cc_start: 0.9357 (p) cc_final: 0.9082 (p) REVERT: A 607 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8395 (mm-30) REVERT: A 640 ASP cc_start: 0.8282 (t70) cc_final: 0.7927 (m-30) REVERT: A 700 ARG cc_start: 0.9009 (pmt-80) cc_final: 0.8702 (ptm160) REVERT: A 757 MET cc_start: 0.8661 (mtp) cc_final: 0.8444 (mmp) REVERT: F 55 ASP cc_start: 0.8816 (m-30) cc_final: 0.8500 (t70) REVERT: F 193 ASP cc_start: 0.7817 (p0) cc_final: 0.7526 (p0) REVERT: F 220 VAL cc_start: 0.9049 (t) cc_final: 0.8636 (p) REVERT: F 332 MET cc_start: 0.9097 (tpt) cc_final: 0.8620 (tpp) REVERT: F 348 ASN cc_start: 0.9255 (p0) cc_final: 0.8856 (p0) REVERT: F 427 MET cc_start: 0.8640 (tmm) cc_final: 0.8402 (ppp) REVERT: F 449 MET cc_start: 0.7903 (ppp) cc_final: 0.7381 (ppp) REVERT: F 450 ASP cc_start: 0.8235 (t70) cc_final: 0.7723 (t0) REVERT: F 478 ASP cc_start: 0.8424 (p0) cc_final: 0.8052 (t70) REVERT: F 498 GLU cc_start: 0.8980 (tt0) cc_final: 0.8712 (mt-10) REVERT: F 603 GLN cc_start: 0.8696 (mm110) cc_final: 0.8241 (mm-40) REVERT: F 757 MET cc_start: 0.8410 (tmm) cc_final: 0.8157 (tmm) REVERT: F 765 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7490 (tmm160) REVERT: E 206 ILE cc_start: 0.9457 (mm) cc_final: 0.9249 (mm) REVERT: E 219 MET cc_start: 0.9401 (mpp) cc_final: 0.9191 (mpp) REVERT: E 410 ASP cc_start: 0.8887 (t0) cc_final: 0.8459 (t0) REVERT: E 414 LEU cc_start: 0.9693 (mt) cc_final: 0.9403 (mt) REVERT: E 462 SER cc_start: 0.9200 (t) cc_final: 0.8513 (t) REVERT: E 466 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8685 (mt-10) REVERT: E 527 LEU cc_start: 0.9109 (mm) cc_final: 0.8787 (mm) REVERT: E 563 PHE cc_start: 0.9307 (m-80) cc_final: 0.8994 (m-80) REVERT: E 574 LEU cc_start: 0.9314 (mm) cc_final: 0.9096 (mm) REVERT: E 611 MET cc_start: 0.8688 (tpt) cc_final: 0.8434 (tpp) REVERT: E 615 LYS cc_start: 0.9395 (mmtt) cc_final: 0.8346 (mtmm) REVERT: E 619 ILE cc_start: 0.9541 (tt) cc_final: 0.9314 (mp) REVERT: E 630 ASP cc_start: 0.9170 (p0) cc_final: 0.8736 (p0) REVERT: E 757 MET cc_start: 0.9313 (ptt) cc_final: 0.9012 (ppp) REVERT: D 219 MET cc_start: 0.8858 (mmp) cc_final: 0.8497 (mmm) REVERT: D 244 TYR cc_start: 0.8129 (p90) cc_final: 0.7224 (p90) REVERT: D 266 PHE cc_start: 0.8068 (t80) cc_final: 0.7799 (t80) REVERT: D 305 GLU cc_start: 0.9004 (tp30) cc_final: 0.8667 (tm-30) REVERT: D 306 LEU cc_start: 0.9463 (tt) cc_final: 0.9127 (tt) REVERT: D 307 ASP cc_start: 0.9290 (p0) cc_final: 0.7505 (t0) REVERT: D 315 LYS cc_start: 0.9229 (mtmm) cc_final: 0.8893 (ptpt) REVERT: D 344 MET cc_start: 0.8987 (tpt) cc_final: 0.8687 (tpp) REVERT: D 417 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8724 (tm-30) REVERT: D 524 LYS cc_start: 0.9523 (ptpp) cc_final: 0.9316 (ptmt) REVERT: D 598 ASP cc_start: 0.8857 (m-30) cc_final: 0.8444 (m-30) REVERT: D 608 MET cc_start: 0.9467 (ttp) cc_final: 0.9106 (ppp) REVERT: D 609 ASP cc_start: 0.8817 (m-30) cc_final: 0.8575 (m-30) REVERT: C 46 MET cc_start: 0.0058 (mtt) cc_final: -0.0343 (mpp) REVERT: C 84 MET cc_start: 0.5686 (ptp) cc_final: 0.4931 (ppp) REVERT: C 305 GLU cc_start: 0.9148 (mm-30) cc_final: 0.8577 (mm-30) REVERT: C 369 ILE cc_start: 0.9656 (mp) cc_final: 0.9451 (tt) REVERT: C 607 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8220 (mt-10) REVERT: C 617 VAL cc_start: 0.9371 (t) cc_final: 0.9151 (t) REVERT: C 689 GLU cc_start: 0.9130 (tt0) cc_final: 0.8862 (mt-10) REVERT: C 736 PHE cc_start: 0.8527 (m-80) cc_final: 0.8208 (m-80) REVERT: C 740 MET cc_start: 0.8679 (ptt) cc_final: 0.8445 (ptt) REVERT: B 138 TYR cc_start: 0.3249 (t80) cc_final: 0.2832 (t80) REVERT: B 274 ILE cc_start: 0.9594 (tp) cc_final: 0.9207 (tp) REVERT: B 275 MET cc_start: 0.9312 (mmp) cc_final: 0.9018 (mmm) REVERT: B 301 ILE cc_start: 0.9277 (tt) cc_final: 0.9063 (tp) REVERT: B 305 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8576 (tm-30) REVERT: B 332 MET cc_start: 0.8885 (ppp) cc_final: 0.8683 (ppp) REVERT: B 379 GLU cc_start: 0.9463 (mt-10) cc_final: 0.9251 (mm-30) REVERT: B 411 LEU cc_start: 0.9744 (mp) cc_final: 0.9538 (mp) REVERT: B 417 GLU cc_start: 0.9453 (tp30) cc_final: 0.8901 (tm-30) REVERT: B 452 PHE cc_start: 0.9020 (m-80) cc_final: 0.8588 (m-10) REVERT: B 538 ASN cc_start: 0.8554 (m-40) cc_final: 0.8302 (t0) REVERT: B 540 ILE cc_start: 0.9211 (mt) cc_final: 0.8984 (mt) REVERT: B 565 LYS cc_start: 0.9327 (ttmm) cc_final: 0.8572 (tppt) REVERT: B 578 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7936 (mm-30) REVERT: B 607 GLU cc_start: 0.9079 (mp0) cc_final: 0.8456 (pt0) REVERT: B 608 MET cc_start: 0.9475 (ppp) cc_final: 0.9257 (ppp) REVERT: B 609 ASP cc_start: 0.8322 (m-30) cc_final: 0.7681 (m-30) REVERT: B 611 MET cc_start: 0.7338 (tpt) cc_final: 0.7106 (tpt) REVERT: B 753 ARG cc_start: 0.9328 (ppt170) cc_final: 0.8899 (ttp80) REVERT: B 757 MET cc_start: 0.9229 (tmm) cc_final: 0.8863 (tmm) outliers start: 2 outliers final: 1 residues processed: 604 average time/residue: 0.2336 time to fit residues: 227.2347 Evaluate side-chains 481 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 480 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 133 optimal weight: 10.0000 chunk 344 optimal weight: 5.9990 chunk 294 optimal weight: 30.0000 chunk 429 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 chunk 319 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 374 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 240 optimal weight: 8.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN F 199 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 384 HIS E 533 ASN E 538 ASN E 568 GLN D 260 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 398 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** B 296 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 = 0.3992 r_free = 0.3992 target = 0.109418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.075952 restraints weight = 143312.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.078121 restraints weight = 98485.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.079559 restraints weight = 74607.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.080601 restraints weight = 61560.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.081298 restraints weight = 53072.534| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 35947 Z= 0.175 Angle : 0.746 10.544 48593 Z= 0.366 Chirality : 0.047 0.192 5470 Planarity : 0.005 0.082 6370 Dihedral : 9.955 161.946 4987 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % 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 are not related in a simple way. whole: -1.55 (0.12), residues: 4424 helix: -0.03 (0.12), residues: 1732 sheet: -0.79 (0.22), residues: 566 loop : -1.97 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 741 TYR 0.017 0.002 TYR F 244 PHE 0.040 0.002 PHE E 736 TRP 0.007 0.001 TRP A 476 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00366 (35947) covalent geometry : angle 0.74560 (48593) hydrogen bonds : bond 0.03571 ( 1235) hydrogen bonds : angle 5.43289 ( 3633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 593 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.7924 (tpt) cc_final: 0.7631 (tpp) REVERT: A 241 ILE cc_start: 0.9462 (mm) cc_final: 0.9060 (tp) REVERT: A 274 ILE cc_start: 0.9778 (mt) cc_final: 0.9552 (mt) REVERT: A 305 GLU cc_start: 0.8296 (tp30) cc_final: 0.7531 (tp30) REVERT: A 321 GLU cc_start: 0.9230 (mp0) cc_final: 0.8873 (mp0) REVERT: A 331 LEU cc_start: 0.9298 (mt) cc_final: 0.9042 (mt) REVERT: A 344 MET cc_start: 0.9047 (mmt) cc_final: 0.8481 (mmt) REVERT: A 388 MET cc_start: 0.8245 (ppp) cc_final: 0.7750 (ppp) REVERT: A 392 ASP cc_start: 0.8692 (t0) cc_final: 0.8432 (t0) REVERT: A 560 ARG cc_start: 0.9060 (mmm160) cc_final: 0.8541 (mmm160) REVERT: A 567 ARG cc_start: 0.9193 (mmm160) cc_final: 0.8862 (ttp-170) REVERT: A 574 LEU cc_start: 0.9623 (mm) cc_final: 0.9409 (mm) REVERT: A 603 GLN cc_start: 0.9557 (mm-40) cc_final: 0.8811 (mm-40) REVERT: A 607 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8249 (mm-30) REVERT: A 757 MET cc_start: 0.8656 (mtp) cc_final: 0.8432 (mmp) REVERT: F 197 SER cc_start: 0.8214 (t) cc_final: 0.7988 (p) REVERT: F 203 TYR cc_start: 0.8644 (m-80) cc_final: 0.8385 (m-10) REVERT: F 220 VAL cc_start: 0.8977 (t) cc_final: 0.8550 (p) REVERT: F 251 LYS cc_start: 0.9366 (ptmt) cc_final: 0.9137 (ptpp) REVERT: F 332 MET cc_start: 0.9089 (tpt) cc_final: 0.8624 (tpp) REVERT: F 337 GLN cc_start: 0.8749 (tm-30) cc_final: 0.8474 (tm-30) REVERT: F 348 ASN cc_start: 0.9295 (p0) cc_final: 0.8772 (p0) REVERT: F 357 LEU cc_start: 0.9516 (mm) cc_final: 0.9302 (mm) REVERT: F 427 MET cc_start: 0.8700 (tmm) cc_final: 0.8476 (ppp) REVERT: F 442 MET cc_start: 0.7545 (mtm) cc_final: 0.7124 (tmm) REVERT: F 449 MET cc_start: 0.7836 (ppp) cc_final: 0.7342 (ppp) REVERT: F 450 ASP cc_start: 0.8296 (t70) cc_final: 0.7788 (t0) REVERT: F 478 ASP cc_start: 0.8433 (p0) cc_final: 0.7988 (t70) REVERT: F 498 GLU cc_start: 0.8991 (tt0) cc_final: 0.8711 (mt-10) REVERT: F 765 ARG cc_start: 0.8116 (tpp80) cc_final: 0.7473 (tmm160) REVERT: E 206 ILE cc_start: 0.9445 (mm) cc_final: 0.9228 (mm) REVERT: E 291 GLU cc_start: 0.8983 (mp0) cc_final: 0.8487 (mp0) REVERT: E 304 ASP cc_start: 0.7513 (t0) cc_final: 0.7308 (t0) REVERT: E 328 LEU cc_start: 0.9774 (tt) cc_final: 0.9565 (tt) REVERT: E 410 ASP cc_start: 0.8895 (t0) cc_final: 0.8433 (t0) REVERT: E 414 LEU cc_start: 0.9685 (mt) cc_final: 0.9408 (mt) REVERT: E 508 MET cc_start: 0.8039 (tmm) cc_final: 0.7711 (tmm) REVERT: E 527 LEU cc_start: 0.8988 (mm) cc_final: 0.8770 (mm) REVERT: E 563 PHE cc_start: 0.9260 (m-80) cc_final: 0.8923 (m-80) REVERT: E 614 LYS cc_start: 0.8582 (tptt) cc_final: 0.7955 (tppt) REVERT: E 615 LYS cc_start: 0.9347 (mmtt) cc_final: 0.8950 (mmtt) REVERT: E 619 ILE cc_start: 0.9560 (tt) cc_final: 0.9330 (mp) REVERT: E 630 ASP cc_start: 0.9044 (p0) cc_final: 0.8681 (p0) REVERT: E 757 MET cc_start: 0.9300 (ptt) cc_final: 0.9017 (ppp) REVERT: D 219 MET cc_start: 0.8842 (mmp) cc_final: 0.8425 (mmm) REVERT: D 306 LEU cc_start: 0.9458 (tt) cc_final: 0.9254 (tt) REVERT: D 315 LYS cc_start: 0.9189 (mtmm) cc_final: 0.8864 (mttt) REVERT: D 344 MET cc_start: 0.8921 (tpt) cc_final: 0.8492 (tpp) REVERT: D 417 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8725 (tm-30) REVERT: D 598 ASP cc_start: 0.8870 (m-30) cc_final: 0.8436 (m-30) REVERT: D 608 MET cc_start: 0.9519 (ttp) cc_final: 0.8972 (ppp) REVERT: D 609 ASP cc_start: 0.8562 (m-30) cc_final: 0.7920 (m-30) REVERT: C 46 MET cc_start: 0.0084 (mtt) cc_final: -0.0297 (mpp) REVERT: C 84 MET cc_start: 0.5714 (ptp) cc_final: 0.4968 (ppp) REVERT: C 305 GLU cc_start: 0.9169 (mm-30) cc_final: 0.8540 (mm-30) REVERT: C 332 MET cc_start: 0.8451 (tmm) cc_final: 0.8127 (tmm) REVERT: C 449 MET cc_start: 0.9100 (mtp) cc_final: 0.8783 (tpp) REVERT: C 607 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8252 (mt-10) REVERT: C 611 MET cc_start: 0.8745 (ptp) cc_final: 0.8539 (ptp) REVERT: C 680 ASN cc_start: 0.8722 (p0) cc_final: 0.8075 (t0) REVERT: C 689 GLU cc_start: 0.9150 (tt0) cc_final: 0.8863 (mt-10) REVERT: C 736 PHE cc_start: 0.8551 (m-80) cc_final: 0.8228 (m-80) REVERT: C 740 MET cc_start: 0.8526 (ptt) cc_final: 0.8271 (ptt) REVERT: B 138 TYR cc_start: 0.3040 (t80) cc_final: 0.2628 (t80) REVERT: B 274 ILE cc_start: 0.9578 (tp) cc_final: 0.9157 (tp) REVERT: B 275 MET cc_start: 0.9223 (mmp) cc_final: 0.8924 (mmm) REVERT: B 301 ILE cc_start: 0.9305 (tt) cc_final: 0.9098 (tp) REVERT: B 305 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8586 (tm-30) REVERT: B 332 MET cc_start: 0.8857 (ppp) cc_final: 0.8631 (ppp) REVERT: B 349 ARG cc_start: 0.9258 (mtp-110) cc_final: 0.8785 (mtm110) REVERT: B 379 GLU cc_start: 0.9509 (mt-10) cc_final: 0.9269 (mm-30) REVERT: B 417 GLU cc_start: 0.9432 (tp30) cc_final: 0.8871 (tm-30) REVERT: B 452 PHE cc_start: 0.9056 (m-80) cc_final: 0.8581 (m-10) REVERT: B 516 PHE cc_start: 0.9270 (m-10) cc_final: 0.8726 (m-10) REVERT: B 538 ASN cc_start: 0.8611 (m-40) cc_final: 0.8296 (t0) REVERT: B 540 ILE cc_start: 0.9239 (mt) cc_final: 0.8828 (mm) REVERT: B 565 LYS cc_start: 0.9198 (ttmm) cc_final: 0.8632 (tppt) REVERT: B 578 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7661 (mm-30) REVERT: B 607 GLU cc_start: 0.9252 (mp0) cc_final: 0.8387 (pt0) REVERT: B 609 ASP cc_start: 0.8324 (m-30) cc_final: 0.7699 (m-30) REVERT: B 620 ILE cc_start: 0.9692 (mt) cc_final: 0.9123 (tt) REVERT: B 741 ARG cc_start: 0.8766 (mmm-85) cc_final: 0.8107 (tpp80) REVERT: B 753 ARG cc_start: 0.9415 (ppt170) cc_final: 0.9000 (ttp80) REVERT: B 757 MET cc_start: 0.9257 (tmm) cc_final: 0.8929 (tmm) outliers start: 2 outliers final: 1 residues processed: 595 average time/residue: 0.2210 time to fit residues: 212.2096 Evaluate side-chains 484 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 483 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 225 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 284 optimal weight: 30.0000 chunk 382 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 154 optimal weight: 20.0000 chunk 165 optimal weight: 0.9980 chunk 413 optimal weight: 10.0000 chunk 365 optimal weight: 20.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN F 384 HIS ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 384 HIS E 533 ASN E 538 ASN E 568 GLN D 260 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 494 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN C 533 ASN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.110054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076348 restraints weight = 142974.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.078531 restraints weight = 97798.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.079951 restraints weight = 74208.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080993 restraints weight = 61606.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.081616 restraints weight = 52836.219| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 35947 Z= 0.148 Angle : 0.737 11.881 48593 Z= 0.358 Chirality : 0.047 0.193 5470 Planarity : 0.005 0.077 6370 Dihedral : 9.919 162.546 4987 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % 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 are not related in a simple way. whole: -1.46 (0.13), residues: 4424 helix: 0.06 (0.12), residues: 1730 sheet: -0.80 (0.22), residues: 569 loop : -1.91 (0.13), residues: 2125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 465 TYR 0.019 0.002 TYR F 517 PHE 0.040 0.002 PHE F 563 TRP 0.014 0.001 TRP A 551 HIS 0.005 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00320 (35947) covalent geometry : angle 0.73736 (48593) hydrogen bonds : bond 0.03438 ( 1235) hydrogen bonds : angle 5.36203 ( 3633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ILE cc_start: 0.9456 (mm) cc_final: 0.9125 (tp) REVERT: A 305 GLU cc_start: 0.8304 (tp30) cc_final: 0.7547 (tp30) REVERT: A 321 GLU cc_start: 0.9270 (mp0) cc_final: 0.8934 (mp0) REVERT: A 331 LEU cc_start: 0.9214 (mt) cc_final: 0.9004 (mt) REVERT: A 344 MET cc_start: 0.9020 (mmt) cc_final: 0.8290 (mmt) REVERT: A 388 MET cc_start: 0.8212 (ppp) cc_final: 0.7653 (ppp) REVERT: A 392 ASP cc_start: 0.8785 (t0) cc_final: 0.8526 (t0) REVERT: A 516 PHE cc_start: 0.8943 (m-80) cc_final: 0.8741 (m-80) REVERT: A 560 ARG cc_start: 0.9135 (mmm160) cc_final: 0.8586 (mmm-85) REVERT: A 567 ARG cc_start: 0.9217 (mmm160) cc_final: 0.8885 (ttp-170) REVERT: A 603 GLN cc_start: 0.9571 (mm-40) cc_final: 0.8819 (mm-40) REVERT: A 607 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8367 (mm-30) REVERT: A 700 ARG cc_start: 0.9017 (pmt-80) cc_final: 0.8814 (ptm160) REVERT: A 757 MET cc_start: 0.8661 (mtp) cc_final: 0.8432 (mmp) REVERT: F 203 TYR cc_start: 0.8623 (m-80) cc_final: 0.8386 (m-10) REVERT: F 220 VAL cc_start: 0.9001 (t) cc_final: 0.8602 (p) REVERT: F 222 LEU cc_start: 0.8971 (mt) cc_final: 0.8713 (mt) REVERT: F 332 MET cc_start: 0.9089 (tpt) cc_final: 0.8644 (tpp) REVERT: F 333 ASP cc_start: 0.8574 (m-30) cc_final: 0.8355 (m-30) REVERT: F 337 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8479 (tm-30) REVERT: F 425 LYS cc_start: 0.9379 (ttmt) cc_final: 0.9085 (pttm) REVERT: F 427 MET cc_start: 0.8544 (tmm) cc_final: 0.8313 (ppp) REVERT: F 442 MET cc_start: 0.7544 (mtm) cc_final: 0.7106 (tmm) REVERT: F 449 MET cc_start: 0.7810 (ppp) cc_final: 0.7290 (ppp) REVERT: F 450 ASP cc_start: 0.8312 (t70) cc_final: 0.7775 (t0) REVERT: F 478 ASP cc_start: 0.8421 (p0) cc_final: 0.8009 (t70) REVERT: F 498 GLU cc_start: 0.9036 (tt0) cc_final: 0.8811 (mt-10) REVERT: F 609 ASP cc_start: 0.8986 (m-30) cc_final: 0.8762 (m-30) REVERT: F 757 MET cc_start: 0.8514 (tmm) cc_final: 0.8283 (tmm) REVERT: E 183 HIS cc_start: 0.8393 (m-70) cc_final: 0.8164 (m-70) REVERT: E 275 MET cc_start: 0.8876 (mpp) cc_final: 0.8640 (mpp) REVERT: E 328 LEU cc_start: 0.9779 (tt) cc_final: 0.9537 (tt) REVERT: E 410 ASP cc_start: 0.8942 (t0) cc_final: 0.8444 (t0) REVERT: E 414 LEU cc_start: 0.9678 (mt) cc_final: 0.9388 (mt) REVERT: E 527 LEU cc_start: 0.8791 (mm) cc_final: 0.8485 (mm) REVERT: E 607 GLU cc_start: 0.9426 (mm-30) cc_final: 0.8980 (mm-30) REVERT: E 614 LYS cc_start: 0.8644 (tptt) cc_final: 0.8229 (tppt) REVERT: E 615 LYS cc_start: 0.9375 (mmtt) cc_final: 0.9048 (mmtt) REVERT: E 630 ASP cc_start: 0.9109 (p0) cc_final: 0.8794 (p0) REVERT: E 757 MET cc_start: 0.9298 (ptt) cc_final: 0.9016 (ppp) REVERT: D 219 MET cc_start: 0.8734 (mmp) cc_final: 0.8379 (mmm) REVERT: D 244 TYR cc_start: 0.7561 (p90) cc_final: 0.6685 (p90) REVERT: D 315 LYS cc_start: 0.9185 (mtmm) cc_final: 0.8956 (mtpt) REVERT: D 344 MET cc_start: 0.8958 (tpt) cc_final: 0.8518 (tpp) REVERT: D 417 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8748 (tm-30) REVERT: D 564 ASP cc_start: 0.8989 (m-30) cc_final: 0.8631 (m-30) REVERT: D 598 ASP cc_start: 0.8615 (m-30) cc_final: 0.8411 (m-30) REVERT: D 608 MET cc_start: 0.9573 (ttp) cc_final: 0.9000 (ppp) REVERT: D 609 ASP cc_start: 0.8372 (m-30) cc_final: 0.7804 (m-30) REVERT: C 46 MET cc_start: 0.0066 (mtt) cc_final: -0.0316 (mpp) REVERT: C 84 MET cc_start: 0.5687 (ptp) cc_final: 0.5016 (ppp) REVERT: C 222 LEU cc_start: 0.9679 (mm) cc_final: 0.9473 (mm) REVERT: C 305 GLU cc_start: 0.9209 (mm-30) cc_final: 0.8636 (mm-30) REVERT: C 449 MET cc_start: 0.9079 (mtp) cc_final: 0.8869 (mmm) REVERT: C 563 PHE cc_start: 0.9039 (m-10) cc_final: 0.8700 (m-10) REVERT: C 604 ILE cc_start: 0.9563 (mt) cc_final: 0.9283 (mt) REVERT: C 617 VAL cc_start: 0.9388 (t) cc_final: 0.9163 (t) REVERT: C 640 ASP cc_start: 0.8027 (t0) cc_final: 0.7767 (t0) REVERT: C 689 GLU cc_start: 0.9159 (tt0) cc_final: 0.8868 (mt-10) REVERT: C 736 PHE cc_start: 0.8571 (m-80) cc_final: 0.8229 (m-80) REVERT: C 740 MET cc_start: 0.8524 (ptt) cc_final: 0.8276 (ptt) REVERT: B 275 MET cc_start: 0.9233 (mmp) cc_final: 0.9007 (mmm) REVERT: B 301 ILE cc_start: 0.9307 (tt) cc_final: 0.9085 (tp) REVERT: B 305 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8608 (tm-30) REVERT: B 332 MET cc_start: 0.8928 (ppp) cc_final: 0.8720 (ppp) REVERT: B 349 ARG cc_start: 0.9238 (mtp-110) cc_final: 0.8877 (mtp-110) REVERT: B 411 LEU cc_start: 0.9717 (mp) cc_final: 0.9502 (mp) REVERT: B 417 GLU cc_start: 0.9449 (tp30) cc_final: 0.8870 (tm-30) REVERT: B 452 PHE cc_start: 0.9094 (m-80) cc_final: 0.8655 (m-10) REVERT: B 465 ARG cc_start: 0.8774 (ptt-90) cc_final: 0.8485 (ttp-110) REVERT: B 516 PHE cc_start: 0.9217 (m-10) cc_final: 0.8712 (m-10) REVERT: B 538 ASN cc_start: 0.8649 (m-40) cc_final: 0.8323 (t0) REVERT: B 540 ILE cc_start: 0.9221 (mt) cc_final: 0.8831 (mm) REVERT: B 565 LYS cc_start: 0.9190 (ttmm) cc_final: 0.8639 (tppt) REVERT: B 607 GLU cc_start: 0.9178 (mp0) cc_final: 0.8833 (pt0) REVERT: B 608 MET cc_start: 0.9471 (ppp) cc_final: 0.9146 (ppp) REVERT: B 609 ASP cc_start: 0.8174 (m-30) cc_final: 0.7846 (p0) REVERT: B 620 ILE cc_start: 0.9702 (mt) cc_final: 0.9153 (tt) REVERT: B 753 ARG cc_start: 0.9403 (ppt170) cc_final: 0.8816 (ttp80) REVERT: B 757 MET cc_start: 0.9263 (tmm) cc_final: 0.8944 (tmm) outliers start: 0 outliers final: 0 residues processed: 583 average time/residue: 0.2170 time to fit residues: 205.9492 Evaluate side-chains 477 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 477 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 71 optimal weight: 8.9990 chunk 258 optimal weight: 8.9990 chunk 206 optimal weight: 7.9990 chunk 365 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 373 optimal weight: 30.0000 chunk 123 optimal weight: 4.9990 chunk 233 optimal weight: 9.9990 chunk 133 optimal weight: 10.0000 chunk 214 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS A 602 ASN F 36 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN E 568 GLN E 760 GLN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 HIS D 490 GLN ** D 533 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN C 692 GLN ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 GLN I 297 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.104081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072861 restraints weight = 144727.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.074837 restraints weight = 102558.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.076084 restraints weight = 78123.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076861 restraints weight = 67182.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.077381 restraints weight = 58672.105| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 35947 Z= 0.293 Angle : 0.883 11.463 48593 Z= 0.445 Chirality : 0.050 0.278 5470 Planarity : 0.007 0.094 6370 Dihedral : 10.182 165.609 4987 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.02 % 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 are not related in a simple way. whole: -2.00 (0.12), residues: 4424 helix: -0.48 (0.12), residues: 1737 sheet: -1.08 (0.22), residues: 550 loop : -2.13 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG C 560 TYR 0.023 0.002 TYR F 517 PHE 0.046 0.003 PHE C 563 TRP 0.015 0.002 TRP A 476 HIS 0.008 0.002 HIS E 340 Details of bonding type rmsd covalent geometry : bond 0.00587 (35947) covalent geometry : angle 0.88264 (48593) hydrogen bonds : bond 0.04469 ( 1235) hydrogen bonds : angle 6.08239 ( 3633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 544 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 GLU cc_start: 0.8585 (tp30) cc_final: 0.7986 (tp30) REVERT: A 312 LYS cc_start: 0.9533 (tptp) cc_final: 0.9189 (tptp) REVERT: A 321 GLU cc_start: 0.9342 (mp0) cc_final: 0.8995 (mp0) REVERT: A 331 LEU cc_start: 0.9278 (mt) cc_final: 0.9073 (mt) REVERT: A 388 MET cc_start: 0.8577 (ppp) cc_final: 0.8076 (ppp) REVERT: A 392 ASP cc_start: 0.9112 (t0) cc_final: 0.8808 (t0) REVERT: A 560 ARG cc_start: 0.8995 (mmm160) cc_final: 0.8189 (mmm160) REVERT: A 567 ARG cc_start: 0.9252 (mmm160) cc_final: 0.8946 (ttp-170) REVERT: A 603 GLN cc_start: 0.9553 (mm-40) cc_final: 0.8892 (mm-40) REVERT: A 607 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8352 (mm-30) REVERT: A 757 MET cc_start: 0.8816 (mtp) cc_final: 0.8554 (mmp) REVERT: F 220 VAL cc_start: 0.9031 (t) cc_final: 0.8650 (p) REVERT: F 332 MET cc_start: 0.9088 (tpt) cc_final: 0.8625 (tpp) REVERT: F 337 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8496 (tm-30) REVERT: F 425 LYS cc_start: 0.9378 (ttmt) cc_final: 0.9105 (pttm) REVERT: F 427 MET cc_start: 0.8520 (tmm) cc_final: 0.8294 (ppp) REVERT: F 449 MET cc_start: 0.8013 (ppp) cc_final: 0.7430 (ppp) REVERT: F 498 GLU cc_start: 0.9155 (tt0) cc_final: 0.8881 (mt-10) REVERT: F 564 ASP cc_start: 0.9109 (m-30) cc_final: 0.8810 (t0) REVERT: F 599 ARG cc_start: 0.8874 (mtt180) cc_final: 0.8487 (mtm180) REVERT: F 635 ARG cc_start: 0.9549 (ptp90) cc_final: 0.9312 (mpp80) REVERT: E 291 GLU cc_start: 0.8959 (mp0) cc_final: 0.8552 (mp0) REVERT: E 410 ASP cc_start: 0.9018 (t0) cc_final: 0.8583 (t0) REVERT: E 414 LEU cc_start: 0.9719 (mt) cc_final: 0.9441 (mt) REVERT: E 527 LEU cc_start: 0.8820 (mm) cc_final: 0.8451 (mm) REVERT: E 565 LYS cc_start: 0.9472 (mtmm) cc_final: 0.9201 (mttt) REVERT: E 607 GLU cc_start: 0.9427 (mm-30) cc_final: 0.9099 (mm-30) REVERT: E 614 LYS cc_start: 0.8744 (tptt) cc_final: 0.8211 (tppt) REVERT: E 615 LYS cc_start: 0.9405 (mmtt) cc_final: 0.9093 (mmtt) REVERT: E 630 ASP cc_start: 0.9232 (p0) cc_final: 0.8880 (p0) REVERT: E 757 MET cc_start: 0.9392 (ptt) cc_final: 0.8808 (ptp) REVERT: D 219 MET cc_start: 0.8935 (mmp) cc_final: 0.8624 (mmm) REVERT: D 312 LYS cc_start: 0.9617 (mttt) cc_final: 0.9384 (mtpp) REVERT: D 315 LYS cc_start: 0.9107 (mtmm) cc_final: 0.8795 (mtpt) REVERT: D 344 MET cc_start: 0.8985 (tpt) cc_final: 0.8541 (tpp) REVERT: D 417 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8751 (tm-30) REVERT: D 524 LYS cc_start: 0.9625 (ptpp) cc_final: 0.9413 (ptmt) REVERT: D 563 PHE cc_start: 0.9323 (m-10) cc_final: 0.8976 (m-10) REVERT: D 564 ASP cc_start: 0.9106 (m-30) cc_final: 0.8702 (m-30) REVERT: D 567 ARG cc_start: 0.9488 (mtp-110) cc_final: 0.8275 (ttp80) REVERT: D 574 LEU cc_start: 0.9673 (mm) cc_final: 0.9466 (mm) REVERT: D 608 MET cc_start: 0.9626 (ttp) cc_final: 0.9068 (ppp) REVERT: D 609 ASP cc_start: 0.8202 (m-30) cc_final: 0.7934 (m-30) REVERT: C 84 MET cc_start: 0.5936 (ptp) cc_final: 0.5353 (ppp) REVERT: C 344 MET cc_start: 0.8690 (mmp) cc_final: 0.8374 (mmp) REVERT: C 449 MET cc_start: 0.9116 (mtp) cc_final: 0.8752 (mmm) REVERT: C 568 GLN cc_start: 0.9525 (tm-30) cc_final: 0.9275 (tm-30) REVERT: C 611 MET cc_start: 0.9025 (ptp) cc_final: 0.8813 (ptp) REVERT: C 689 GLU cc_start: 0.9039 (tt0) cc_final: 0.8809 (mt-10) REVERT: B 267 PHE cc_start: 0.9247 (t80) cc_final: 0.9026 (t80) REVERT: B 274 ILE cc_start: 0.9603 (tp) cc_final: 0.9238 (tp) REVERT: B 275 MET cc_start: 0.9267 (mmp) cc_final: 0.8953 (mmm) REVERT: B 301 ILE cc_start: 0.9224 (tt) cc_final: 0.8940 (tp) REVERT: B 305 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8623 (tm-30) REVERT: B 349 ARG cc_start: 0.9217 (mtp-110) cc_final: 0.9006 (mtp-110) REVERT: B 379 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9157 (mm-30) REVERT: B 417 GLU cc_start: 0.9502 (tp30) cc_final: 0.8908 (tm-30) REVERT: B 452 PHE cc_start: 0.9188 (m-80) cc_final: 0.8746 (m-10) REVERT: B 516 PHE cc_start: 0.9347 (m-10) cc_final: 0.9027 (m-10) REVERT: B 538 ASN cc_start: 0.8671 (m-40) cc_final: 0.8457 (t0) REVERT: B 540 ILE cc_start: 0.9301 (mt) cc_final: 0.9070 (mt) REVERT: B 565 LYS cc_start: 0.9313 (ttmm) cc_final: 0.8801 (tppt) REVERT: B 607 GLU cc_start: 0.9223 (mp0) cc_final: 0.8295 (pt0) REVERT: B 609 ASP cc_start: 0.8283 (m-30) cc_final: 0.7872 (m-30) REVERT: B 678 MET cc_start: 0.8469 (mtt) cc_final: 0.8009 (mtt) REVERT: B 753 ARG cc_start: 0.9423 (ppt170) cc_final: 0.8922 (ttp80) REVERT: B 757 MET cc_start: 0.9276 (tmm) cc_final: 0.8961 (tmm) outliers start: 1 outliers final: 0 residues processed: 545 average time/residue: 0.2191 time to fit residues: 194.7451 Evaluate side-chains 443 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 83 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 320 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 439 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 182 optimal weight: 9.9990 chunk 146 optimal weight: 8.9990 chunk 370 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 533 ASN E 538 ASN D 90 ASN D 260 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 GLN C 533 ASN C 692 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 345 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.105820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.072467 restraints weight = 144278.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074564 restraints weight = 97873.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.075964 restraints weight = 73850.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.077008 restraints weight = 61078.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.077639 restraints weight = 52938.423| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35947 Z= 0.223 Angle : 0.820 11.439 48593 Z= 0.408 Chirality : 0.049 0.285 5470 Planarity : 0.006 0.077 6370 Dihedral : 10.091 172.198 4987 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % Twisted General : 0.02 % 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 are not related in a simple way. whole: -1.92 (0.12), residues: 4424 helix: -0.41 (0.12), residues: 1752 sheet: -1.08 (0.22), residues: 561 loop : -2.08 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 560 TYR 0.021 0.002 TYR C 244 PHE 0.039 0.002 PHE F 563 TRP 0.009 0.001 TRP A 476 HIS 0.007 0.001 HIS E 226 Details of bonding type rmsd covalent geometry : bond 0.00458 (35947) covalent geometry : angle 0.82005 (48593) hydrogen bonds : bond 0.04074 ( 1235) hydrogen bonds : angle 5.90117 ( 3633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8550 (mt-10) REVERT: A 305 GLU cc_start: 0.8533 (tp30) cc_final: 0.7920 (tp30) REVERT: A 331 LEU cc_start: 0.9153 (mt) cc_final: 0.8943 (mt) REVERT: A 388 MET cc_start: 0.8571 (ppp) cc_final: 0.8036 (ppp) REVERT: A 392 ASP cc_start: 0.9265 (t0) cc_final: 0.8992 (t0) REVERT: A 560 ARG cc_start: 0.9013 (mmm160) cc_final: 0.7880 (mmm160) REVERT: A 565 LYS cc_start: 0.9324 (ptpp) cc_final: 0.9069 (pttm) REVERT: A 567 ARG cc_start: 0.9337 (mmm160) cc_final: 0.9003 (ttp-170) REVERT: A 603 GLN cc_start: 0.9559 (mm-40) cc_final: 0.8593 (mm-40) REVERT: A 606 THR cc_start: 0.9249 (p) cc_final: 0.8984 (p) REVERT: A 607 GLU cc_start: 0.9011 (mm-30) cc_final: 0.8237 (mm-30) REVERT: A 757 MET cc_start: 0.8822 (mtp) cc_final: 0.8544 (mmp) REVERT: F 203 TYR cc_start: 0.8835 (m-80) cc_final: 0.8519 (m-10) REVERT: F 220 VAL cc_start: 0.9086 (t) cc_final: 0.8707 (p) REVERT: F 337 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8503 (tm-30) REVERT: F 425 LYS cc_start: 0.9370 (ttmt) cc_final: 0.8938 (tppt) REVERT: F 427 MET cc_start: 0.8457 (tmm) cc_final: 0.8203 (ppp) REVERT: F 449 MET cc_start: 0.8124 (ppp) cc_final: 0.7413 (ppp) REVERT: F 450 ASP cc_start: 0.8432 (t70) cc_final: 0.7931 (t0) REVERT: F 466 GLU cc_start: 0.9069 (mp0) cc_final: 0.8813 (mp0) REVERT: F 498 GLU cc_start: 0.9240 (tt0) cc_final: 0.8892 (mt-10) REVERT: F 564 ASP cc_start: 0.9178 (m-30) cc_final: 0.8899 (t0) REVERT: F 565 LYS cc_start: 0.8979 (ttmm) cc_final: 0.8774 (ttmm) REVERT: E 206 ILE cc_start: 0.9504 (mm) cc_final: 0.9304 (mm) REVERT: E 291 GLU cc_start: 0.9019 (mp0) cc_final: 0.8572 (pm20) REVERT: E 410 ASP cc_start: 0.9076 (t0) cc_final: 0.8585 (t0) REVERT: E 414 LEU cc_start: 0.9721 (mt) cc_final: 0.9445 (mt) REVERT: E 427 MET cc_start: 0.7005 (ppp) cc_final: 0.6795 (ppp) REVERT: E 565 LYS cc_start: 0.9420 (mtmm) cc_final: 0.9165 (mttt) REVERT: E 598 ASP cc_start: 0.8896 (m-30) cc_final: 0.8473 (m-30) REVERT: E 607 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9093 (mm-30) REVERT: E 614 LYS cc_start: 0.8707 (tptt) cc_final: 0.8122 (tppt) REVERT: E 615 LYS cc_start: 0.9446 (mmtt) cc_final: 0.9162 (mmtt) REVERT: E 630 ASP cc_start: 0.9325 (p0) cc_final: 0.8939 (p0) REVERT: E 757 MET cc_start: 0.9407 (ptt) cc_final: 0.8932 (ptp) REVERT: D 219 MET cc_start: 0.9037 (mmp) cc_final: 0.8657 (mmm) REVERT: D 312 LYS cc_start: 0.9621 (mttt) cc_final: 0.9405 (mtpp) REVERT: D 315 LYS cc_start: 0.9109 (mtmm) cc_final: 0.8744 (mtpt) REVERT: D 332 MET cc_start: 0.8942 (tmm) cc_final: 0.8652 (tmm) REVERT: D 344 MET cc_start: 0.9059 (tpt) cc_final: 0.8563 (tpp) REVERT: D 417 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8778 (tm-30) REVERT: D 564 ASP cc_start: 0.9106 (m-30) cc_final: 0.8834 (m-30) REVERT: D 608 MET cc_start: 0.9667 (ttp) cc_final: 0.9154 (tmm) REVERT: D 609 ASP cc_start: 0.8719 (m-30) cc_final: 0.7781 (m-30) REVERT: C 84 MET cc_start: 0.5877 (ptp) cc_final: 0.5161 (ppp) REVERT: C 302 PHE cc_start: 0.8765 (t80) cc_final: 0.8415 (t80) REVERT: C 344 MET cc_start: 0.8897 (mmp) cc_final: 0.8599 (mmp) REVERT: C 449 MET cc_start: 0.9316 (mtp) cc_final: 0.8895 (mmm) REVERT: C 568 GLN cc_start: 0.9522 (tm-30) cc_final: 0.9293 (tm-30) REVERT: C 604 ILE cc_start: 0.9530 (mm) cc_final: 0.9164 (mm) REVERT: C 609 ASP cc_start: 0.8893 (t0) cc_final: 0.8690 (m-30) REVERT: C 640 ASP cc_start: 0.8363 (t0) cc_final: 0.8015 (t0) REVERT: C 689 GLU cc_start: 0.9148 (tt0) cc_final: 0.8893 (mt-10) REVERT: B 265 PHE cc_start: 0.8420 (m-10) cc_final: 0.8205 (m-80) REVERT: B 267 PHE cc_start: 0.9324 (t80) cc_final: 0.9016 (t80) REVERT: B 274 ILE cc_start: 0.9653 (tp) cc_final: 0.9291 (tp) REVERT: B 275 MET cc_start: 0.9347 (mmp) cc_final: 0.8947 (mmm) REVERT: B 301 ILE cc_start: 0.9275 (tt) cc_final: 0.9054 (tp) REVERT: B 305 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8562 (tm-30) REVERT: B 332 MET cc_start: 0.8970 (ppp) cc_final: 0.8617 (ppp) REVERT: B 349 ARG cc_start: 0.9249 (mtp-110) cc_final: 0.9046 (mtp-110) REVERT: B 368 ASP cc_start: 0.9146 (p0) cc_final: 0.8938 (p0) REVERT: B 379 GLU cc_start: 0.9518 (mm-30) cc_final: 0.9073 (mm-30) REVERT: B 417 GLU cc_start: 0.9550 (tp30) cc_final: 0.8877 (tm-30) REVERT: B 452 PHE cc_start: 0.9310 (m-80) cc_final: 0.8754 (m-10) REVERT: B 470 GLU cc_start: 0.8524 (pt0) cc_final: 0.8236 (pp20) REVERT: B 491 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8631 (mm-30) REVERT: B 516 PHE cc_start: 0.9365 (m-10) cc_final: 0.9030 (m-10) REVERT: B 538 ASN cc_start: 0.8755 (m-40) cc_final: 0.8443 (t0) REVERT: B 540 ILE cc_start: 0.9247 (mt) cc_final: 0.8861 (mm) REVERT: B 565 LYS cc_start: 0.9247 (ttmm) cc_final: 0.8750 (tppt) REVERT: B 753 ARG cc_start: 0.9431 (ppt170) cc_final: 0.8900 (ttp80) REVERT: B 757 MET cc_start: 0.9307 (tmm) cc_final: 0.9021 (tmm) outliers start: 0 outliers final: 0 residues processed: 541 average time/residue: 0.2193 time to fit residues: 194.4120 Evaluate side-chains 447 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 89 optimal weight: 10.0000 chunk 311 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 421 optimal weight: 0.0470 chunk 41 optimal weight: 0.5980 chunk 243 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 405 optimal weight: 0.0870 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 340 HIS A 602 ASN F 199 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 HIS E 533 ASN E 568 GLN D 260 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN B 226 HIS ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 317 HIS ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.110625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076713 restraints weight = 142071.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.078771 restraints weight = 95351.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.080230 restraints weight = 71606.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.081274 restraints weight = 58877.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.081765 restraints weight = 50883.326| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35947 Z= 0.134 Angle : 0.785 12.518 48593 Z= 0.380 Chirality : 0.049 0.228 5470 Planarity : 0.005 0.076 6370 Dihedral : 9.847 178.912 4987 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.81 % 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 are not related in a simple way. whole: -1.62 (0.13), residues: 4424 helix: -0.11 (0.12), residues: 1751 sheet: -0.96 (0.21), residues: 581 loop : -1.95 (0.13), residues: 2092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG F 635 TYR 0.020 0.001 TYR C 244 PHE 0.048 0.002 PHE E 736 TRP 0.014 0.001 TRP F 551 HIS 0.010 0.001 HIS E 735 Details of bonding type rmsd covalent geometry : bond 0.00297 (35947) covalent geometry : angle 0.78470 (48593) hydrogen bonds : bond 0.03500 ( 1235) hydrogen bonds : angle 5.54562 ( 3633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8848 Ramachandran restraints generated. 4424 Oldfield, 0 Emsley, 4424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 585 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 241 ILE cc_start: 0.9642 (mm) cc_final: 0.9316 (tp) REVERT: A 305 GLU cc_start: 0.8815 (tp30) cc_final: 0.8053 (tp30) REVERT: A 331 LEU cc_start: 0.9111 (mt) cc_final: 0.8873 (mt) REVERT: A 344 MET cc_start: 0.9045 (mmp) cc_final: 0.8466 (mmp) REVERT: A 388 MET cc_start: 0.8618 (ppp) cc_final: 0.8034 (ppp) REVERT: A 392 ASP cc_start: 0.9149 (t0) cc_final: 0.8830 (t0) REVERT: A 460 ASN cc_start: 0.9070 (t0) cc_final: 0.8654 (t0) REVERT: A 516 PHE cc_start: 0.9201 (m-80) cc_final: 0.8930 (m-80) REVERT: A 560 ARG cc_start: 0.9094 (mmm160) cc_final: 0.8430 (mmm160) REVERT: A 565 LYS cc_start: 0.9301 (ptpp) cc_final: 0.9046 (pttm) REVERT: A 567 ARG cc_start: 0.9318 (mmm160) cc_final: 0.8954 (ttp-170) REVERT: A 574 LEU cc_start: 0.9625 (mm) cc_final: 0.9401 (mm) REVERT: A 603 GLN cc_start: 0.9561 (mm-40) cc_final: 0.8549 (mm-40) REVERT: A 606 THR cc_start: 0.9172 (p) cc_final: 0.8882 (p) REVERT: A 607 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8090 (mm-30) REVERT: A 700 ARG cc_start: 0.9192 (pmt-80) cc_final: 0.8655 (ttt180) REVERT: A 740 MET cc_start: 0.8476 (ptp) cc_final: 0.8258 (ptp) REVERT: A 757 MET cc_start: 0.8684 (mtp) cc_final: 0.8439 (mmp) REVERT: F 203 TYR cc_start: 0.8794 (m-80) cc_final: 0.8453 (m-10) REVERT: F 220 VAL cc_start: 0.8901 (t) cc_final: 0.8516 (p) REVERT: F 251 LYS cc_start: 0.9463 (ptmt) cc_final: 0.9190 (ptpp) REVERT: F 332 MET cc_start: 0.9122 (tpt) cc_final: 0.8609 (tpt) REVERT: F 337 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8521 (tm-30) REVERT: F 347 THR cc_start: 0.8579 (t) cc_final: 0.8150 (t) REVERT: F 360 PHE cc_start: 0.8439 (m-10) cc_final: 0.8236 (m-10) REVERT: F 417 GLU cc_start: 0.8957 (tp30) cc_final: 0.8540 (tp30) REVERT: F 425 LYS cc_start: 0.9332 (ttmt) cc_final: 0.9010 (pttm) REVERT: F 427 MET cc_start: 0.8599 (tmm) cc_final: 0.8353 (ppp) REVERT: F 449 MET cc_start: 0.8079 (ppp) cc_final: 0.7517 (ppp) REVERT: F 498 GLU cc_start: 0.9162 (tt0) cc_final: 0.8827 (mt-10) REVERT: F 562 ILE cc_start: 0.9409 (mm) cc_final: 0.9122 (mm) REVERT: F 609 ASP cc_start: 0.9059 (m-30) cc_final: 0.8837 (m-30) REVERT: E 211 LYS cc_start: 0.9517 (mppt) cc_final: 0.9239 (pttt) REVERT: E 216 ILE cc_start: 0.9506 (mp) cc_final: 0.9214 (mp) REVERT: E 291 GLU cc_start: 0.8983 (mp0) cc_final: 0.8562 (mp0) REVERT: E 301 ILE cc_start: 0.9657 (mm) cc_final: 0.9370 (mt) REVERT: E 410 ASP cc_start: 0.9007 (t0) cc_final: 0.8454 (t0) REVERT: E 414 LEU cc_start: 0.9665 (mt) cc_final: 0.9398 (mt) REVERT: E 427 MET cc_start: 0.6937 (ppp) cc_final: 0.6730 (ppp) REVERT: E 565 LYS cc_start: 0.9398 (mtmm) cc_final: 0.9141 (ptpp) REVERT: E 607 GLU cc_start: 0.9367 (mm-30) cc_final: 0.9112 (mm-30) REVERT: E 614 LYS cc_start: 0.8664 (tptt) cc_final: 0.8111 (tppt) REVERT: E 615 LYS cc_start: 0.9420 (mmtt) cc_final: 0.9144 (mmtt) REVERT: E 630 ASP cc_start: 0.9248 (p0) cc_final: 0.8879 (p0) REVERT: E 757 MET cc_start: 0.9428 (ptt) cc_final: 0.9156 (ppp) REVERT: D 205 ASP cc_start: 0.9063 (t70) cc_final: 0.8845 (t0) REVERT: D 244 TYR cc_start: 0.8249 (p90) cc_final: 0.7284 (p90) REVERT: D 291 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8788 (pt0) REVERT: D 312 LYS cc_start: 0.9616 (mttt) cc_final: 0.9275 (mtpp) REVERT: D 315 LYS cc_start: 0.9203 (mtmm) cc_final: 0.8881 (mtpt) REVERT: D 344 MET cc_start: 0.9004 (tpt) cc_final: 0.8518 (tpp) REVERT: D 414 LEU cc_start: 0.9176 (mt) cc_final: 0.8948 (mt) REVERT: D 417 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8709 (tm-30) REVERT: D 564 ASP cc_start: 0.9060 (m-30) cc_final: 0.8811 (m-30) REVERT: D 608 MET cc_start: 0.9638 (ttp) cc_final: 0.9095 (ppp) REVERT: D 609 ASP cc_start: 0.8460 (m-30) cc_final: 0.7633 (m-30) REVERT: D 678 MET cc_start: 0.8908 (mmm) cc_final: 0.8513 (mtt) REVERT: C 46 MET cc_start: -0.0060 (mtt) cc_final: -0.0463 (mpp) REVERT: C 84 MET cc_start: 0.5753 (ptp) cc_final: 0.5061 (ppp) REVERT: C 449 MET cc_start: 0.8948 (mtp) cc_final: 0.8675 (mmm) REVERT: C 568 GLN cc_start: 0.9479 (tm-30) cc_final: 0.9243 (tm-30) REVERT: C 611 MET cc_start: 0.9189 (ptp) cc_final: 0.8848 (ptp) REVERT: C 689 GLU cc_start: 0.9144 (tt0) cc_final: 0.8821 (mt-10) REVERT: B 267 PHE cc_start: 0.9287 (t80) cc_final: 0.8995 (t80) REVERT: B 301 ILE cc_start: 0.9264 (tt) cc_final: 0.9031 (tp) REVERT: B 305 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 332 MET cc_start: 0.8882 (ppp) cc_final: 0.8580 (ppp) REVERT: B 349 ARG cc_start: 0.9300 (mtp-110) cc_final: 0.8978 (mtp-110) REVERT: B 379 GLU cc_start: 0.9507 (mm-30) cc_final: 0.9017 (mm-30) REVERT: B 417 GLU cc_start: 0.9529 (tp30) cc_final: 0.8818 (tm-30) REVERT: B 452 PHE cc_start: 0.9274 (m-80) cc_final: 0.8686 (m-10) REVERT: B 464 LEU cc_start: 0.9442 (pt) cc_final: 0.8830 (pt) REVERT: B 465 ARG cc_start: 0.9218 (ptt-90) cc_final: 0.8906 (ptp90) REVERT: B 470 GLU cc_start: 0.8430 (pt0) cc_final: 0.8080 (pp20) REVERT: B 491 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 516 PHE cc_start: 0.9282 (m-10) cc_final: 0.8804 (m-10) REVERT: B 538 ASN cc_start: 0.8760 (m-40) cc_final: 0.8444 (t0) REVERT: B 540 ILE cc_start: 0.9254 (mt) cc_final: 0.8946 (mm) REVERT: B 565 LYS cc_start: 0.9175 (ttmm) cc_final: 0.8645 (tppt) REVERT: B 608 MET cc_start: 0.9564 (ppp) cc_final: 0.9221 (ppp) REVERT: B 620 ILE cc_start: 0.9679 (mt) cc_final: 0.9034 (tt) REVERT: B 753 ARG cc_start: 0.9445 (ppt170) cc_final: 0.9073 (ttp80) REVERT: B 757 MET cc_start: 0.9307 (tmm) cc_final: 0.8994 (tmm) outliers start: 0 outliers final: 0 residues processed: 585 average time/residue: 0.2189 time to fit residues: 210.2949 Evaluate side-chains 473 residues out of total 3820 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 304 optimal weight: 20.0000 chunk 216 optimal weight: 20.0000 chunk 96 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 401 optimal weight: 6.9990 chunk 362 optimal weight: 20.0000 chunk 326 optimal weight: 4.9990 chunk 257 optimal weight: 20.0000 chunk 202 optimal weight: 0.6980 chunk 302 optimal weight: 1.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 602 ASN ** E 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 533 ASN E 538 ASN D 260 ASN ** D 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 533 ASN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.107499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074669 restraints weight = 142913.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.076647 restraints weight = 98307.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.078082 restraints weight = 74059.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.079069 restraints weight = 60192.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.079781 restraints weight = 52300.560| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 35947 Z= 0.179 Angle : 0.788 11.301 48593 Z= 0.389 Chirality : 0.048 0.217 5470 Planarity : 0.005 0.076 6370 Dihedral : 9.842 179.736 4987 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 18.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.02 % Twisted Proline : 0.41 % 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 are not related in a simple way. whole: -1.66 (0.13), residues: 4424 helix: -0.17 (0.12), residues: 1764 sheet: -1.03 (0.21), residues: 579 loop : -1.94 (0.14), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 362 TYR 0.016 0.002 TYR C 244 PHE 0.033 0.002 PHE C 618 TRP 0.013 0.001 TRP F 476 HIS 0.006 0.001 HIS A 115 Details of bonding type rmsd covalent geometry : bond 0.00382 (35947) covalent geometry : angle 0.78825 (48593) hydrogen bonds : bond 0.03709 ( 1235) hydrogen bonds : angle 5.72243 ( 3633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7505.29 seconds wall clock time: 129 minutes 52.16 seconds (7792.16 seconds total)