Starting phenix.real_space_refine on Tue Aug 26 23:16:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6m_42996/08_2025/8v6m_42996_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6m_42996/08_2025/8v6m_42996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v6m_42996/08_2025/8v6m_42996_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6m_42996/08_2025/8v6m_42996_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v6m_42996/08_2025/8v6m_42996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6m_42996/08_2025/8v6m_42996.map" } resolution = 3.63 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= 0.004 sd= 0.031 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 S 128 5.16 5 Na 3 4.78 5 C 14124 2.51 5 N 3468 2.21 5 O 3812 1.98 5 H 21092 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42639 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10482 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "B" Number of atoms: 10482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10482 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "C" Number of atoms: 10482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10482 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "D" Number of atoms: 10482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10482 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {' NA': 3, 'I8E': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'I8E': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'I8E': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'I8E': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.67, per 1000 atoms: 0.16 Number of scatterers: 42639 At special positions: 0 Unit cell: (141.93, 141.93, 131.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 128 16.00 P 12 15.00 Na 3 11.00 O 3812 8.00 N 3468 7.00 C 14124 6.00 H 21092 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 612 " - pdb=" SG CYS A 619 " distance=2.03 Simple disulfide: pdb=" SG CYS A 721 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 612 " - pdb=" SG CYS B 619 " distance=2.03 Simple disulfide: pdb=" SG CYS B 721 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 612 " - pdb=" SG CYS C 619 " distance=2.03 Simple disulfide: pdb=" SG CYS C 721 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS D 612 " - pdb=" SG CYS D 619 " distance=2.03 Simple disulfide: pdb=" SG CYS D 721 " - pdb=" SG CYS D 731 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.98 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 8 sheets defined 63.8% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 117 through 130 removed outlier: 3.501A pdb=" N GLU A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 149 removed outlier: 3.512A pdb=" N LEU A 138 " --> pdb=" O GLU A 134 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG A 147 " --> pdb=" O GLN A 143 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 161 Processing helix chain 'A' and resid 170 through 178 removed outlier: 3.867A pdb=" N ASN A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.691A pdb=" N ARG A 188 " --> pdb=" O LYS A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 206 removed outlier: 3.508A pdb=" N ILE A 204 " --> pdb=" O LEU A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.589A pdb=" N LEU A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 272 removed outlier: 3.559A pdb=" N LEU A 268 " --> pdb=" O THR A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 284 Processing helix chain 'A' and resid 298 through 306 removed outlier: 3.507A pdb=" N ALA A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 3.663A pdb=" N LEU A 325 " --> pdb=" O TYR A 321 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 removed outlier: 3.553A pdb=" N THR A 336 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 352 Processing helix chain 'A' and resid 353 through 362 removed outlier: 3.541A pdb=" N LEU A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 Processing helix chain 'A' and resid 402 through 410 removed outlier: 3.915A pdb=" N VAL A 408 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 removed outlier: 3.794A pdb=" N MET A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 420 " --> pdb=" O ARG A 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 415 through 420' Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.542A pdb=" N LYS A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 460 Processing helix chain 'A' and resid 480 through 507 removed outlier: 3.574A pdb=" N GLY A 486 " --> pdb=" O LEU A 482 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE A 503 " --> pdb=" O VAL A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 543 removed outlier: 3.795A pdb=" N PHE A 524 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 525 " --> pdb=" O TRP A 521 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 563 removed outlier: 3.704A pdb=" N CYS A 550 " --> pdb=" O GLU A 546 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 553 " --> pdb=" O ALA A 549 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 563 " --> pdb=" O TRP A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 removed outlier: 3.807A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 609 removed outlier: 3.883A pdb=" N VAL A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 603 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 604 " --> pdb=" O GLY A 600 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 617 removed outlier: 3.683A pdb=" N LYS A 617 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 638 removed outlier: 3.712A pdb=" N LEU A 630 " --> pdb=" O SER A 626 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE A 637 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 638 " --> pdb=" O LYS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 707 removed outlier: 4.119A pdb=" N LEU A 658 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 681 " --> pdb=" O MET A 677 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLU A 682 " --> pdb=" O GLY A 678 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER A 685 " --> pdb=" O VAL A 681 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS A 686 " --> pdb=" O GLU A 682 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLU A 689 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 690 " --> pdb=" O LYS A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 Processing helix chain 'B' and resid 118 through 130 removed outlier: 3.500A pdb=" N GLU B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 149 removed outlier: 3.513A pdb=" N LEU B 138 " --> pdb=" O GLU B 134 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 147 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG B 148 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 161 Processing helix chain 'B' and resid 170 through 178 removed outlier: 3.868A pdb=" N ASN B 178 " --> pdb=" O LYS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.691A pdb=" N ARG B 188 " --> pdb=" O LYS B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 206 removed outlier: 3.507A pdb=" N ILE B 204 " --> pdb=" O LEU B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.589A pdb=" N LEU B 233 " --> pdb=" O ASP B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 272 removed outlier: 3.559A pdb=" N LEU B 268 " --> pdb=" O THR B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 284 Processing helix chain 'B' and resid 298 through 306 removed outlier: 3.506A pdb=" N ALA B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 329 removed outlier: 3.664A pdb=" N LEU B 325 " --> pdb=" O TYR B 321 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.553A pdb=" N THR B 336 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 352 Processing helix chain 'B' and resid 353 through 362 removed outlier: 3.542A pdb=" N LEU B 357 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.916A pdb=" N VAL B 408 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 removed outlier: 3.795A pdb=" N MET B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU B 420 " --> pdb=" O ARG B 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 415 through 420' Processing helix chain 'B' and resid 425 through 436 removed outlier: 3.542A pdb=" N LYS B 432 " --> pdb=" O LEU B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 460 Processing helix chain 'B' and resid 480 through 507 removed outlier: 3.575A pdb=" N GLY B 486 " --> pdb=" O LEU B 482 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE B 503 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 543 removed outlier: 3.796A pdb=" N PHE B 524 " --> pdb=" O ALA B 520 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL B 525 " --> pdb=" O TRP B 521 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA B 543 " --> pdb=" O LEU B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 563 removed outlier: 3.705A pdb=" N CYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 553 " --> pdb=" O ALA B 549 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 563 " --> pdb=" O TRP B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 583 removed outlier: 3.807A pdb=" N GLN B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 609 removed outlier: 3.882A pdb=" N VAL B 596 " --> pdb=" O PHE B 592 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL B 603 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 604 " --> pdb=" O GLY B 600 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE B 609 " --> pdb=" O LEU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 617 removed outlier: 3.684A pdb=" N LYS B 617 " --> pdb=" O LYS B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 638 removed outlier: 3.712A pdb=" N LEU B 630 " --> pdb=" O SER B 626 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 635 " --> pdb=" O GLU B 631 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 637 " --> pdb=" O PHE B 633 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 638 " --> pdb=" O LYS B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 707 removed outlier: 4.119A pdb=" N LEU B 658 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 668 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 681 " --> pdb=" O MET B 677 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU B 682 " --> pdb=" O GLY B 678 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER B 685 " --> pdb=" O VAL B 681 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS B 686 " --> pdb=" O GLU B 682 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLU B 689 " --> pdb=" O SER B 685 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG B 690 " --> pdb=" O LYS B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 Processing helix chain 'C' and resid 118 through 130 removed outlier: 3.501A pdb=" N GLU C 129 " --> pdb=" O ALA C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 149 removed outlier: 3.513A pdb=" N LEU C 138 " --> pdb=" O GLU C 134 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG C 147 " --> pdb=" O GLN C 143 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ARG C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 161 Processing helix chain 'C' and resid 170 through 178 removed outlier: 3.867A pdb=" N ASN C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.691A pdb=" N ARG C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 206 removed outlier: 3.507A pdb=" N ILE C 204 " --> pdb=" O LEU C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.589A pdb=" N LEU C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 272 removed outlier: 3.559A pdb=" N LEU C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 284 Processing helix chain 'C' and resid 298 through 306 removed outlier: 3.506A pdb=" N ALA C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 329 removed outlier: 3.664A pdb=" N LEU C 325 " --> pdb=" O TYR C 321 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG C 327 " --> pdb=" O MET C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.553A pdb=" N THR C 336 " --> pdb=" O LEU C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 352 Processing helix chain 'C' and resid 353 through 362 removed outlier: 3.541A pdb=" N LEU C 357 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 Processing helix chain 'C' and resid 402 through 410 removed outlier: 3.916A pdb=" N VAL C 408 " --> pdb=" O LEU C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.795A pdb=" N MET C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 420 " --> pdb=" O ARG C 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 415 through 420' Processing helix chain 'C' and resid 425 through 436 removed outlier: 3.541A pdb=" N LYS C 432 " --> pdb=" O LEU C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 460 Processing helix chain 'C' and resid 480 through 507 removed outlier: 3.574A pdb=" N GLY C 486 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY C 502 " --> pdb=" O SER C 498 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE C 503 " --> pdb=" O VAL C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 543 removed outlier: 3.794A pdb=" N PHE C 524 " --> pdb=" O ALA C 520 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL C 525 " --> pdb=" O TRP C 521 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 563 removed outlier: 3.704A pdb=" N CYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 553 " --> pdb=" O ALA C 549 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 563 " --> pdb=" O TRP C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 583 removed outlier: 3.807A pdb=" N GLN C 580 " --> pdb=" O SER C 576 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 609 removed outlier: 3.884A pdb=" N VAL C 596 " --> pdb=" O PHE C 592 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 603 " --> pdb=" O LEU C 599 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA C 604 " --> pdb=" O GLY C 600 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 617 removed outlier: 3.683A pdb=" N LYS C 617 " --> pdb=" O LYS C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 638 removed outlier: 3.712A pdb=" N LEU C 630 " --> pdb=" O SER C 626 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 635 " --> pdb=" O GLU C 631 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE C 637 " --> pdb=" O PHE C 633 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY C 638 " --> pdb=" O LYS C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 707 removed outlier: 4.119A pdb=" N LEU C 658 " --> pdb=" O PHE C 654 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU C 668 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL C 681 " --> pdb=" O MET C 677 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N GLU C 682 " --> pdb=" O GLY C 678 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER C 685 " --> pdb=" O VAL C 681 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LYS C 686 " --> pdb=" O GLU C 682 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLU C 689 " --> pdb=" O SER C 685 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG C 690 " --> pdb=" O LYS C 686 " (cutoff:3.500A) Processing helix chain 'C' and resid 708 through 715 Processing helix chain 'D' and resid 118 through 130 removed outlier: 3.501A pdb=" N GLU D 129 " --> pdb=" O ALA D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 149 removed outlier: 3.513A pdb=" N LEU D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG D 147 " --> pdb=" O GLN D 143 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ARG D 148 " --> pdb=" O GLU D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 161 Processing helix chain 'D' and resid 170 through 178 removed outlier: 3.868A pdb=" N ASN D 178 " --> pdb=" O LYS D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.690A pdb=" N ARG D 188 " --> pdb=" O LYS D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 199 through 206 removed outlier: 3.508A pdb=" N ILE D 204 " --> pdb=" O LEU D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 223 Processing helix chain 'D' and resid 227 through 237 removed outlier: 3.589A pdb=" N LEU D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 272 removed outlier: 3.559A pdb=" N LEU D 268 " --> pdb=" O THR D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 284 Processing helix chain 'D' and resid 298 through 306 removed outlier: 3.506A pdb=" N ALA D 302 " --> pdb=" O ASN D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 329 removed outlier: 3.664A pdb=" N LEU D 325 " --> pdb=" O TYR D 321 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.553A pdb=" N THR D 336 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 353 through 362 removed outlier: 3.541A pdb=" N LEU D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 374 Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.916A pdb=" N VAL D 408 " --> pdb=" O LEU D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 420 removed outlier: 3.795A pdb=" N MET D 419 " --> pdb=" O ASN D 415 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 420 " --> pdb=" O ARG D 416 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 415 through 420' Processing helix chain 'D' and resid 425 through 436 removed outlier: 3.542A pdb=" N LYS D 432 " --> pdb=" O LEU D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 436 through 460 Processing helix chain 'D' and resid 480 through 507 removed outlier: 3.575A pdb=" N GLY D 486 " --> pdb=" O LEU D 482 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY D 502 " --> pdb=" O SER D 498 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE D 503 " --> pdb=" O VAL D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 543 removed outlier: 3.795A pdb=" N PHE D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL D 525 " --> pdb=" O TRP D 521 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA D 543 " --> pdb=" O LEU D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 563 removed outlier: 3.704A pdb=" N CYS D 550 " --> pdb=" O GLU D 546 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 553 " --> pdb=" O ALA D 549 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 563 " --> pdb=" O TRP D 559 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 583 removed outlier: 3.807A pdb=" N GLN D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 609 removed outlier: 3.884A pdb=" N VAL D 596 " --> pdb=" O PHE D 592 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 603 " --> pdb=" O LEU D 599 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA D 604 " --> pdb=" O GLY D 600 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 617 removed outlier: 3.682A pdb=" N LYS D 617 " --> pdb=" O LYS D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 624 through 638 removed outlier: 3.712A pdb=" N LEU D 630 " --> pdb=" O SER D 626 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU D 635 " --> pdb=" O GLU D 631 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE D 637 " --> pdb=" O PHE D 633 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY D 638 " --> pdb=" O LYS D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 707 removed outlier: 4.119A pdb=" N LEU D 658 " --> pdb=" O PHE D 654 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL D 681 " --> pdb=" O MET D 677 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLU D 682 " --> pdb=" O GLY D 678 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER D 685 " --> pdb=" O VAL D 681 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LYS D 686 " --> pdb=" O GLU D 682 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N GLU D 689 " --> pdb=" O SER D 685 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG D 690 " --> pdb=" O LYS D 686 " (cutoff:3.500A) Processing helix chain 'D' and resid 708 through 715 Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 382 removed outlier: 6.838A pdb=" N SER A 387 " --> pdb=" O ASP A 379 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA A 381 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL A 385 " --> pdb=" O ALA A 381 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 386 " --> pdb=" O GLU A 736 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER A 388 " --> pdb=" O ILE A 734 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR A 390 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 721 through 724 removed outlier: 5.807A pdb=" N LYS A 722 " --> pdb=" O ARG A 729 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ARG A 729 " --> pdb=" O LYS A 722 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA A 724 " --> pdb=" O ASP A 727 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP A 727 " --> pdb=" O ALA A 724 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 376 through 382 removed outlier: 6.838A pdb=" N SER B 387 " --> pdb=" O ASP B 379 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ALA B 381 " --> pdb=" O VAL B 385 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL B 385 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 386 " --> pdb=" O GLU B 736 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 388 " --> pdb=" O ILE B 734 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 390 " --> pdb=" O LEU B 732 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 721 through 724 removed outlier: 5.806A pdb=" N LYS B 722 " --> pdb=" O ARG B 729 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG B 729 " --> pdb=" O LYS B 722 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA B 724 " --> pdb=" O ASP B 727 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP B 727 " --> pdb=" O ALA B 724 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 376 through 382 removed outlier: 6.838A pdb=" N SER C 387 " --> pdb=" O ASP C 379 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA C 381 " --> pdb=" O VAL C 385 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 386 " --> pdb=" O GLU C 736 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER C 388 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR C 390 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 721 through 724 removed outlier: 5.807A pdb=" N LYS C 722 " --> pdb=" O ARG C 729 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG C 729 " --> pdb=" O LYS C 722 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA C 724 " --> pdb=" O ASP C 727 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP C 727 " --> pdb=" O ALA C 724 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 376 through 382 removed outlier: 6.838A pdb=" N SER D 387 " --> pdb=" O ASP D 379 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA D 381 " --> pdb=" O VAL D 385 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL D 385 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER D 386 " --> pdb=" O GLU D 736 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER D 388 " --> pdb=" O ILE D 734 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR D 390 " --> pdb=" O LEU D 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 721 through 724 removed outlier: 5.807A pdb=" N LYS D 722 " --> pdb=" O ARG D 729 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N ARG D 729 " --> pdb=" O LYS D 722 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA D 724 " --> pdb=" O ASP D 727 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP D 727 " --> pdb=" O ALA D 724 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 1021 hydrogen bonds defined for protein. 3003 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: 7.90 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 21064 1.03 - 1.23: 326 1.23 - 1.43: 8760 1.43 - 1.63: 12734 1.63 - 1.83: 212 Bond restraints: 43096 Sorted by residual: bond pdb=" O12 POV B 904 " pdb=" P POV B 904 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.49e+00 bond pdb=" O12 POV A 904 " pdb=" P POV A 904 " ideal model delta sigma weight residual 1.657 1.595 0.062 2.00e-02 2.50e+03 9.47e+00 bond pdb=" O12 POV D 901 " pdb=" P POV D 901 " ideal model delta sigma weight residual 1.657 1.596 0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" O12 POV C 904 " pdb=" P POV C 904 " ideal model delta sigma weight residual 1.657 1.596 0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" O12 POV B 902 " pdb=" P POV B 902 " ideal model delta sigma weight residual 1.657 1.596 0.061 2.00e-02 2.50e+03 9.34e+00 ... (remaining 43091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.19: 77409 5.19 - 10.37: 122 10.37 - 15.56: 5 15.56 - 20.74: 0 20.74 - 25.93: 12 Bond angle restraints: 77548 Sorted by residual: angle pdb=" CG2 VAL B 681 " pdb=" CB VAL B 681 " pdb=" HB VAL B 681 " ideal model delta sigma weight residual 108.00 82.07 25.93 3.00e+00 1.11e-01 7.47e+01 angle pdb=" CG2 VAL D 681 " pdb=" CB VAL D 681 " pdb=" HB VAL D 681 " ideal model delta sigma weight residual 108.00 82.12 25.88 3.00e+00 1.11e-01 7.44e+01 angle pdb=" CG2 VAL C 681 " pdb=" CB VAL C 681 " pdb=" HB VAL C 681 " ideal model delta sigma weight residual 108.00 82.15 25.85 3.00e+00 1.11e-01 7.42e+01 angle pdb=" CG2 VAL A 681 " pdb=" CB VAL A 681 " pdb=" HB VAL A 681 " ideal model delta sigma weight residual 108.00 82.15 25.85 3.00e+00 1.11e-01 7.42e+01 angle pdb=" CG1 VAL C 681 " pdb=" CB VAL C 681 " pdb=" HB VAL C 681 " ideal model delta sigma weight residual 108.00 82.17 25.83 3.00e+00 1.11e-01 7.41e+01 ... (remaining 77543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 20016 35.59 - 71.18: 371 71.18 - 106.77: 25 106.77 - 142.36: 8 142.36 - 177.95: 8 Dihedral angle restraints: 20428 sinusoidal: 11272 harmonic: 9156 Sorted by residual: dihedral pdb=" CA GLN C 570 " pdb=" C GLN C 570 " pdb=" N SER C 571 " pdb=" CA SER C 571 " ideal model delta harmonic sigma weight residual -180.00 -129.75 -50.25 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA GLN A 570 " pdb=" C GLN A 570 " pdb=" N SER A 571 " pdb=" CA SER A 571 " ideal model delta harmonic sigma weight residual 180.00 -129.82 -50.18 0 5.00e+00 4.00e-02 1.01e+02 dihedral pdb=" CA GLN D 570 " pdb=" C GLN D 570 " pdb=" N SER D 571 " pdb=" CA SER D 571 " ideal model delta harmonic sigma weight residual -180.00 -129.83 -50.17 0 5.00e+00 4.00e-02 1.01e+02 ... (remaining 20425 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.311: 3292 0.311 - 0.622: 0 0.622 - 0.933: 0 0.933 - 1.244: 0 1.244 - 1.554: 4 Chirality restraints: 3296 Sorted by residual: chirality pdb=" CB VAL A 681 " pdb=" CA VAL A 681 " pdb=" CG1 VAL A 681 " pdb=" CG2 VAL A 681 " both_signs ideal model delta sigma weight residual False -2.63 -1.07 -1.55 2.00e-01 2.50e+01 6.04e+01 chirality pdb=" CB VAL D 681 " pdb=" CA VAL D 681 " pdb=" CG1 VAL D 681 " pdb=" CG2 VAL D 681 " both_signs ideal model delta sigma weight residual False -2.63 -1.08 -1.55 2.00e-01 2.50e+01 6.03e+01 chirality pdb=" CB VAL C 681 " pdb=" CA VAL C 681 " pdb=" CG1 VAL C 681 " pdb=" CG2 VAL C 681 " both_signs ideal model delta sigma weight residual False -2.63 -1.08 -1.55 2.00e-01 2.50e+01 6.03e+01 ... (remaining 3293 not shown) Planarity restraints: 6132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 529 " -0.103 2.00e-02 2.50e+03 1.08e-01 1.75e+02 pdb=" CD GLN A 529 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN A 529 " 0.089 2.00e-02 2.50e+03 pdb=" NE2 GLN A 529 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN A 529 " 0.154 2.00e-02 2.50e+03 pdb="HE22 GLN A 529 " -0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 529 " 0.102 2.00e-02 2.50e+03 1.08e-01 1.75e+02 pdb=" CD GLN B 529 " -0.020 2.00e-02 2.50e+03 pdb=" OE1 GLN B 529 " -0.089 2.00e-02 2.50e+03 pdb=" NE2 GLN B 529 " -0.004 2.00e-02 2.50e+03 pdb="HE21 GLN B 529 " -0.154 2.00e-02 2.50e+03 pdb="HE22 GLN B 529 " 0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 529 " -0.103 2.00e-02 2.50e+03 1.08e-01 1.75e+02 pdb=" CD GLN D 529 " 0.021 2.00e-02 2.50e+03 pdb=" OE1 GLN D 529 " 0.089 2.00e-02 2.50e+03 pdb=" NE2 GLN D 529 " 0.004 2.00e-02 2.50e+03 pdb="HE21 GLN D 529 " 0.154 2.00e-02 2.50e+03 pdb="HE22 GLN D 529 " -0.165 2.00e-02 2.50e+03 ... (remaining 6129 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 4048 2.26 - 2.85: 96797 2.85 - 3.43: 106159 3.43 - 4.02: 143177 4.02 - 4.60: 222547 Nonbonded interactions: 572728 Sorted by model distance: nonbonded pdb=" OD1 ASN A 298 " pdb=" HD1 HIS A 301 " model vdw 1.680 2.450 nonbonded pdb=" OD1 ASN C 298 " pdb=" HD1 HIS C 301 " model vdw 1.680 2.450 nonbonded pdb=" OH TYR A 460 " pdb=" H PHE B 625 " model vdw 1.712 2.450 nonbonded pdb="HH21 ARG C 292 " pdb=" O ASN C 338 " model vdw 1.720 2.450 nonbonded pdb="HH21 ARG D 292 " pdb=" O ASN D 338 " model vdw 1.721 2.450 ... (remaining 572723 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 117 through 902) selection = (chain 'B' and resid 117 through 902) selection = (chain 'C' and resid 117 through 902) selection = (chain 'D' and resid 117 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=0.45 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: 1.050 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: 0.260 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 32.620 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.050 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:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.006 0.062 22012 Z= 0.290 Angle : 1.067 11.317 29688 Z= 0.591 Chirality : 0.070 1.554 3296 Planarity : 0.006 0.105 3644 Dihedral : 14.484 177.948 8464 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 1.10 % Allowed : 10.66 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.80 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.72 (0.14), residues: 2552 helix: -2.77 (0.10), residues: 1404 sheet: -4.48 (0.30), residues: 120 loop : -3.32 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 464 TYR 0.016 0.001 TYR C 564 PHE 0.016 0.002 PHE A 316 TRP 0.011 0.001 TRP B 331 HIS 0.007 0.001 HIS B 523 Details of bonding type rmsd covalent geometry : bond 0.00599 (22004) covalent geometry : angle 1.06651 (29672) SS BOND : bond 0.00069 ( 8) SS BOND : angle 1.37927 ( 16) hydrogen bonds : bond 0.31947 ( 1021) hydrogen bonds : angle 9.61583 ( 3003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 700 time to evaluate : 0.684 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 282 MET cc_start: 0.8969 (tpp) cc_final: 0.8010 (tpt) REVERT: A 336 THR cc_start: 0.9187 (m) cc_final: 0.8776 (p) REVERT: A 409 TYR cc_start: 0.7729 (m-80) cc_final: 0.7475 (m-80) REVERT: B 282 MET cc_start: 0.8984 (tpp) cc_final: 0.8110 (tpt) REVERT: B 336 THR cc_start: 0.9191 (m) cc_final: 0.8837 (p) REVERT: B 409 TYR cc_start: 0.7750 (m-80) cc_final: 0.7541 (m-80) REVERT: C 282 MET cc_start: 0.8940 (tpp) cc_final: 0.8054 (tpt) REVERT: C 336 THR cc_start: 0.9202 (m) cc_final: 0.8825 (p) REVERT: C 409 TYR cc_start: 0.7732 (m-80) cc_final: 0.7495 (m-80) REVERT: D 282 MET cc_start: 0.9053 (tpp) cc_final: 0.8175 (tpt) REVERT: D 336 THR cc_start: 0.9131 (m) cc_final: 0.8709 (p) REVERT: D 409 TYR cc_start: 0.7743 (m-80) cc_final: 0.7439 (m-80) outliers start: 0 outliers final: 0 residues processed: 700 average time/residue: 0.3965 time to fit residues: 393.5748 Evaluate side-chains 368 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN A 242 ASN A 251 ASN A 401 ASN A 452 ASN A 647 ASN A 735 ASN B 227 GLN B 242 ASN B 251 ASN B 401 ASN B 452 ASN B 647 ASN B 735 ASN C 227 GLN C 242 ASN C 251 ASN C 401 ASN C 452 ASN C 647 ASN C 735 ASN D 242 ASN D 251 ASN D 401 ASN D 452 ASN D 647 ASN D 735 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.170694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129994 restraints weight = 80376.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138150 restraints weight = 34476.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.142759 restraints weight = 20906.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.146524 restraints weight = 15273.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.147937 restraints weight = 12278.807| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3727 r_free = 0.3727 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22012 Z= 0.179 Angle : 0.768 10.931 29688 Z= 0.402 Chirality : 0.064 1.467 3296 Planarity : 0.005 0.071 3644 Dihedral : 16.119 178.603 3424 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.94 % Allowed : 10.34 % Favored : 88.71 % Rotamer: Outliers : 2.82 % Allowed : 10.98 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.76 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.15), residues: 2552 helix: -0.60 (0.12), residues: 1524 sheet: -3.61 (0.43), residues: 76 loop : -3.75 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 698 TYR 0.012 0.001 TYR D 540 PHE 0.014 0.002 PHE A 316 TRP 0.005 0.001 TRP A 739 HIS 0.005 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00402 (22004) covalent geometry : angle 0.76197 (29672) SS BOND : bond 0.00529 ( 8) SS BOND : angle 4.12836 ( 16) hydrogen bonds : bond 0.06697 ( 1021) hydrogen bonds : angle 5.01509 ( 3003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 376 time to evaluate : 0.882 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: A 336 THR cc_start: 0.9089 (m) cc_final: 0.8592 (p) REVERT: A 555 MET cc_start: 0.7381 (mtm) cc_final: 0.7017 (mtm) REVERT: B 336 THR cc_start: 0.9087 (m) cc_final: 0.8581 (p) REVERT: B 555 MET cc_start: 0.7303 (mtm) cc_final: 0.6926 (mtm) REVERT: C 336 THR cc_start: 0.9092 (m) cc_final: 0.8586 (p) REVERT: C 555 MET cc_start: 0.7351 (mtm) cc_final: 0.6999 (mtm) REVERT: C 677 MET cc_start: 0.7811 (ttp) cc_final: 0.7469 (mmm) REVERT: D 336 THR cc_start: 0.9072 (m) cc_final: 0.8552 (p) outliers start: 64 outliers final: 48 residues processed: 414 average time/residue: 0.2779 time to fit residues: 183.2692 Evaluate side-chains 349 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 301 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 609 ILE Chi-restraints excluded: chain A residue 645 GLN Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 645 GLN Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 671 ASN Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 645 GLN Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 671 ASN Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 645 GLN Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 671 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 203 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 239 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 401 ASN C 401 ASN D 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.164039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.122313 restraints weight = 81178.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129411 restraints weight = 36184.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134044 restraints weight = 22693.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.136929 restraints weight = 17064.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.138712 restraints weight = 14260.434| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 22012 Z= 0.182 Angle : 0.706 11.088 29688 Z= 0.369 Chirality : 0.062 1.450 3296 Planarity : 0.004 0.057 3644 Dihedral : 15.288 165.271 3424 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.63 % Allowed : 11.32 % Favored : 88.05 % Rotamer: Outliers : 2.95 % Allowed : 12.48 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.48 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.64 (0.17), residues: 2552 helix: 0.49 (0.13), residues: 1532 sheet: -2.93 (0.46), residues: 92 loop : -3.74 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 567 TYR 0.018 0.002 TYR D 460 PHE 0.017 0.002 PHE B 524 TRP 0.012 0.001 TRP C 559 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00412 (22004) covalent geometry : angle 0.70216 (29672) SS BOND : bond 0.00981 ( 8) SS BOND : angle 3.12916 ( 16) hydrogen bonds : bond 0.05418 ( 1021) hydrogen bonds : angle 4.43763 ( 3003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 327 time to evaluate : 0.815 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: A 336 THR cc_start: 0.9189 (m) cc_final: 0.8705 (p) REVERT: A 409 TYR cc_start: 0.7913 (m-80) cc_final: 0.7595 (m-80) REVERT: B 336 THR cc_start: 0.9202 (m) cc_final: 0.8721 (p) REVERT: B 409 TYR cc_start: 0.7912 (m-80) cc_final: 0.7614 (m-80) REVERT: B 592 PHE cc_start: 0.8127 (t80) cc_final: 0.7916 (t80) REVERT: B 728 PHE cc_start: 0.8222 (m-10) cc_final: 0.8022 (m-80) REVERT: C 336 THR cc_start: 0.9212 (m) cc_final: 0.8733 (p) REVERT: C 409 TYR cc_start: 0.7915 (m-80) cc_final: 0.7590 (m-80) REVERT: D 336 THR cc_start: 0.9200 (m) cc_final: 0.8719 (p) REVERT: D 409 TYR cc_start: 0.7925 (m-80) cc_final: 0.7604 (m-80) REVERT: D 555 MET cc_start: 0.7560 (mtm) cc_final: 0.7359 (mtm) REVERT: D 592 PHE cc_start: 0.8127 (t80) cc_final: 0.7916 (t80) REVERT: D 728 PHE cc_start: 0.8237 (m-10) cc_final: 0.8027 (m-80) outliers start: 67 outliers final: 36 residues processed: 367 average time/residue: 0.2865 time to fit residues: 167.8259 Evaluate side-chains 326 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 290 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 648 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 82 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 142 optimal weight: 5.9990 chunk 36 optimal weight: 8.9990 chunk 121 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 251 ASN A 401 ASN B 178 ASN B 251 ASN B 401 ASN C 178 ASN C 251 ASN C 401 ASN D 178 ASN D 251 ASN D 401 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.118847 restraints weight = 81110.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.125613 restraints weight = 36956.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130065 restraints weight = 23525.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132880 restraints weight = 17864.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.134657 restraints weight = 14992.055| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3584 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 22012 Z= 0.187 Angle : 0.679 11.309 29688 Z= 0.355 Chirality : 0.062 1.446 3296 Planarity : 0.004 0.054 3644 Dihedral : 14.389 166.036 3424 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.05 % Favored : 88.48 % Rotamer: Outliers : 2.91 % Allowed : 13.93 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.37 (0.17), residues: 2552 helix: 0.78 (0.13), residues: 1532 sheet: -3.40 (0.40), residues: 112 loop : -3.69 (0.19), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 567 TYR 0.012 0.001 TYR D 451 PHE 0.018 0.002 PHE D 316 TRP 0.010 0.001 TRP D 559 HIS 0.004 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00426 (22004) covalent geometry : angle 0.67476 (29672) SS BOND : bond 0.00794 ( 8) SS BOND : angle 3.16921 ( 16) hydrogen bonds : bond 0.04757 ( 1021) hydrogen bonds : angle 4.33686 ( 3003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 330 time to evaluate : 0.764 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: A 336 THR cc_start: 0.9210 (m) cc_final: 0.8776 (p) REVERT: A 409 TYR cc_start: 0.7969 (m-80) cc_final: 0.7692 (m-80) REVERT: A 631 GLU cc_start: 0.8347 (tp30) cc_final: 0.8089 (tp30) REVERT: B 336 THR cc_start: 0.9208 (m) cc_final: 0.8774 (p) REVERT: B 409 TYR cc_start: 0.7920 (m-80) cc_final: 0.7646 (m-80) REVERT: B 631 GLU cc_start: 0.8365 (tp30) cc_final: 0.8116 (tp30) REVERT: C 336 THR cc_start: 0.9210 (m) cc_final: 0.8774 (p) REVERT: C 409 TYR cc_start: 0.7965 (m-80) cc_final: 0.7685 (m-80) REVERT: C 631 GLU cc_start: 0.8368 (tp30) cc_final: 0.8114 (tp30) REVERT: D 165 SER cc_start: 0.8791 (m) cc_final: 0.8558 (t) REVERT: D 336 THR cc_start: 0.9195 (m) cc_final: 0.8757 (p) REVERT: D 409 TYR cc_start: 0.7963 (m-80) cc_final: 0.7682 (m-80) REVERT: D 631 GLU cc_start: 0.8370 (tp30) cc_final: 0.8112 (tp30) outliers start: 66 outliers final: 46 residues processed: 368 average time/residue: 0.2889 time to fit residues: 171.6253 Evaluate side-chains 351 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 305 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 545 LYS Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 545 LYS Chi-restraints excluded: chain C residue 583 ILE Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 232 optimal weight: 4.9990 chunk 137 optimal weight: 7.9990 chunk 177 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 238 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN B 401 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 401 ASN D 251 ASN D 401 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.159246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.117416 restraints weight = 80678.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.124081 restraints weight = 36823.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.128460 restraints weight = 23441.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131254 restraints weight = 17787.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133025 restraints weight = 14925.350| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.6100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22012 Z= 0.181 Angle : 0.665 11.049 29688 Z= 0.347 Chirality : 0.061 1.436 3296 Planarity : 0.005 0.103 3644 Dihedral : 13.939 166.043 3424 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.78 % Favored : 88.75 % Rotamer: Outliers : 3.70 % Allowed : 13.76 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.17), residues: 2552 helix: 0.93 (0.13), residues: 1528 sheet: -3.13 (0.49), residues: 88 loop : -3.73 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 567 TYR 0.014 0.001 TYR B 213 PHE 0.018 0.001 PHE A 316 TRP 0.009 0.001 TRP D 559 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00420 (22004) covalent geometry : angle 0.66353 (29672) SS BOND : bond 0.00330 ( 8) SS BOND : angle 2.28272 ( 16) hydrogen bonds : bond 0.04778 ( 1021) hydrogen bonds : angle 4.31813 ( 3003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 320 time to evaluate : 0.772 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 165 SER cc_start: 0.8713 (m) cc_final: 0.8447 (t) REVERT: A 336 THR cc_start: 0.9245 (m) cc_final: 0.8829 (p) REVERT: A 631 GLU cc_start: 0.8389 (tp30) cc_final: 0.8153 (tp30) REVERT: B 336 THR cc_start: 0.9245 (m) cc_final: 0.8828 (p) REVERT: B 631 GLU cc_start: 0.8425 (tp30) cc_final: 0.8175 (tp30) REVERT: B 682 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7062 (pt0) REVERT: C 336 THR cc_start: 0.9253 (m) cc_final: 0.8833 (p) REVERT: C 631 GLU cc_start: 0.8418 (tp30) cc_final: 0.8168 (tp30) REVERT: D 165 SER cc_start: 0.8725 (m) cc_final: 0.8451 (t) REVERT: D 336 THR cc_start: 0.9243 (m) cc_final: 0.8825 (p) REVERT: D 351 MET cc_start: 0.8136 (mtt) cc_final: 0.7914 (mtt) REVERT: D 631 GLU cc_start: 0.8371 (tp30) cc_final: 0.8130 (tp30) outliers start: 84 outliers final: 52 residues processed: 385 average time/residue: 0.2749 time to fit residues: 170.2743 Evaluate side-chains 354 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 302 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 713 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 40 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 223 optimal weight: 0.4980 chunk 192 optimal weight: 10.0000 chunk 162 optimal weight: 5.9990 chunk 236 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 ASN B 286 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 286 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.158838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116467 restraints weight = 81788.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.123070 restraints weight = 37854.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127432 restraints weight = 24320.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130243 restraints weight = 18549.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131999 restraints weight = 15604.291| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.6377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22012 Z= 0.167 Angle : 0.645 11.222 29688 Z= 0.335 Chirality : 0.061 1.460 3296 Planarity : 0.005 0.113 3644 Dihedral : 13.564 161.951 3424 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.32 % Favored : 88.52 % Rotamer: Outliers : 3.00 % Allowed : 15.08 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.17), residues: 2552 helix: 1.10 (0.13), residues: 1524 sheet: -3.00 (0.49), residues: 88 loop : -3.70 (0.18), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 567 TYR 0.013 0.001 TYR C 540 PHE 0.019 0.001 PHE D 316 TRP 0.009 0.001 TRP B 710 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd covalent geometry : bond 0.00389 (22004) covalent geometry : angle 0.64384 (29672) SS BOND : bond 0.00786 ( 8) SS BOND : angle 2.09492 ( 16) hydrogen bonds : bond 0.04508 ( 1021) hydrogen bonds : angle 4.23730 ( 3003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 306 time to evaluate : 0.879 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 336 THR cc_start: 0.9258 (m) cc_final: 0.8877 (p) REVERT: A 631 GLU cc_start: 0.8363 (tp30) cc_final: 0.8127 (tp30) REVERT: B 336 THR cc_start: 0.9257 (m) cc_final: 0.8866 (p) REVERT: B 631 GLU cc_start: 0.8402 (tp30) cc_final: 0.8155 (tp30) REVERT: C 336 THR cc_start: 0.9263 (m) cc_final: 0.8878 (p) REVERT: C 631 GLU cc_start: 0.8391 (tp30) cc_final: 0.8138 (tp30) REVERT: D 336 THR cc_start: 0.9253 (m) cc_final: 0.8869 (p) REVERT: D 351 MET cc_start: 0.8113 (mtt) cc_final: 0.7899 (mtt) REVERT: D 631 GLU cc_start: 0.8358 (tp30) cc_final: 0.8125 (tp30) outliers start: 68 outliers final: 56 residues processed: 352 average time/residue: 0.2894 time to fit residues: 164.5436 Evaluate side-chains 348 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 292 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 713 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 35 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 chunk 157 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 244 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 chunk 191 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN B 251 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN C 286 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN D 251 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.159797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.117139 restraints weight = 81575.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123788 restraints weight = 37816.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128230 restraints weight = 24380.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130979 restraints weight = 18597.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132720 restraints weight = 15723.560| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3561 r_free = 0.3561 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22012 Z= 0.142 Angle : 0.626 10.505 29688 Z= 0.324 Chirality : 0.061 1.433 3296 Planarity : 0.005 0.112 3644 Dihedral : 13.116 151.370 3424 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.85 % Favored : 88.99 % Rotamer: Outliers : 2.95 % Allowed : 15.52 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.82 (0.17), residues: 2552 helix: 1.28 (0.13), residues: 1520 sheet: -2.85 (0.51), residues: 88 loop : -3.60 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.013 0.001 TYR C 540 PHE 0.019 0.001 PHE D 316 TRP 0.008 0.001 TRP C 739 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00323 (22004) covalent geometry : angle 0.62525 (29672) SS BOND : bond 0.00369 ( 8) SS BOND : angle 1.79709 ( 16) hydrogen bonds : bond 0.04292 ( 1021) hydrogen bonds : angle 4.08289 ( 3003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 303 time to evaluate : 1.075 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: A 159 MET cc_start: 0.7237 (mmm) cc_final: 0.7034 (mmm) REVERT: A 336 THR cc_start: 0.9277 (m) cc_final: 0.8956 (p) REVERT: A 631 GLU cc_start: 0.8275 (tp30) cc_final: 0.8014 (tp30) REVERT: B 159 MET cc_start: 0.7234 (mmm) cc_final: 0.7033 (mmm) REVERT: B 336 THR cc_start: 0.9261 (m) cc_final: 0.8954 (p) REVERT: B 631 GLU cc_start: 0.8383 (tp30) cc_final: 0.8102 (tp30) REVERT: C 159 MET cc_start: 0.7263 (mmm) cc_final: 0.7039 (mmm) REVERT: C 336 THR cc_start: 0.9284 (m) cc_final: 0.8958 (p) REVERT: C 631 GLU cc_start: 0.8384 (tp30) cc_final: 0.8162 (tp30) REVERT: D 336 THR cc_start: 0.9261 (m) cc_final: 0.8953 (p) REVERT: D 351 MET cc_start: 0.8108 (mtt) cc_final: 0.7887 (mtt) REVERT: D 631 GLU cc_start: 0.8313 (tp30) cc_final: 0.8045 (tp30) outliers start: 67 outliers final: 62 residues processed: 347 average time/residue: 0.2751 time to fit residues: 154.0688 Evaluate side-chains 350 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 288 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 569 PHE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 569 PHE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 401 ASN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 713 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 28 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 165 optimal weight: 10.0000 chunk 189 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 chunk 149 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN B 251 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.116396 restraints weight = 82179.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.122962 restraints weight = 38084.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127344 restraints weight = 24539.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130112 restraints weight = 18743.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131750 restraints weight = 15819.114| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.6657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22012 Z= 0.156 Angle : 0.629 10.808 29688 Z= 0.325 Chirality : 0.061 1.440 3296 Planarity : 0.005 0.119 3644 Dihedral : 12.879 142.112 3424 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.40 % Favored : 88.44 % Rotamer: Outliers : 3.35 % Allowed : 15.43 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.78 (0.17), residues: 2552 helix: 1.32 (0.13), residues: 1520 sheet: -2.83 (0.50), residues: 88 loop : -3.58 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 567 TYR 0.012 0.001 TYR C 540 PHE 0.018 0.001 PHE D 316 TRP 0.008 0.001 TRP D 710 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00361 (22004) covalent geometry : angle 0.62783 (29672) SS BOND : bond 0.00377 ( 8) SS BOND : angle 1.71940 ( 16) hydrogen bonds : bond 0.04301 ( 1021) hydrogen bonds : angle 4.11035 ( 3003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 305 time to evaluate : 1.126 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: A 322 ASP cc_start: 0.8358 (t70) cc_final: 0.7840 (t0) REVERT: A 336 THR cc_start: 0.9286 (m) cc_final: 0.8966 (p) REVERT: A 631 GLU cc_start: 0.8291 (tp30) cc_final: 0.8052 (tp30) REVERT: B 322 ASP cc_start: 0.8357 (t70) cc_final: 0.7844 (t0) REVERT: B 336 THR cc_start: 0.9288 (m) cc_final: 0.8962 (p) REVERT: B 582 VAL cc_start: 0.6899 (OUTLIER) cc_final: 0.6456 (t) REVERT: B 631 GLU cc_start: 0.8366 (tp30) cc_final: 0.8158 (tp30) REVERT: C 336 THR cc_start: 0.9289 (m) cc_final: 0.8970 (p) REVERT: C 631 GLU cc_start: 0.8358 (tp30) cc_final: 0.8147 (tp30) REVERT: D 322 ASP cc_start: 0.8347 (t70) cc_final: 0.7835 (t0) REVERT: D 336 THR cc_start: 0.9286 (m) cc_final: 0.8960 (p) REVERT: D 351 MET cc_start: 0.8075 (mtt) cc_final: 0.7864 (mtt) REVERT: D 631 GLU cc_start: 0.8281 (tp30) cc_final: 0.8036 (tp30) outliers start: 76 outliers final: 69 residues processed: 352 average time/residue: 0.2930 time to fit residues: 165.4187 Evaluate side-chains 363 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 293 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 551 LEU Chi-restraints excluded: chain B residue 569 PHE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 177 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 551 LEU Chi-restraints excluded: chain C residue 569 PHE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 713 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 713 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 187 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 153 optimal weight: 0.0370 chunk 203 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 225 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 overall best weight: 1.1460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.162224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.119393 restraints weight = 81336.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126202 restraints weight = 37695.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130704 restraints weight = 24184.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133539 restraints weight = 18418.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.135310 restraints weight = 15508.787| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3592 r_free = 0.3592 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.6793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22012 Z= 0.117 Angle : 0.607 10.763 29688 Z= 0.310 Chirality : 0.061 1.463 3296 Planarity : 0.005 0.117 3644 Dihedral : 11.945 118.868 3424 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.70 % Favored : 89.15 % Rotamer: Outliers : 2.51 % Allowed : 16.23 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.17), residues: 2552 helix: 1.58 (0.13), residues: 1520 sheet: -2.63 (0.53), residues: 88 loop : -3.48 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 567 TYR 0.012 0.001 TYR C 540 PHE 0.021 0.001 PHE A 316 TRP 0.009 0.001 TRP C 739 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00261 (22004) covalent geometry : angle 0.60666 (29672) SS BOND : bond 0.00294 ( 8) SS BOND : angle 1.33095 ( 16) hydrogen bonds : bond 0.03875 ( 1021) hydrogen bonds : angle 3.91017 ( 3003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 311 time to evaluate : 0.895 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: A 336 THR cc_start: 0.9266 (m) cc_final: 0.8964 (p) REVERT: B 336 THR cc_start: 0.9243 (m) cc_final: 0.8959 (p) REVERT: B 569 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: B 570 GLN cc_start: 0.7243 (mm-40) cc_final: 0.5765 (pm20) REVERT: B 582 VAL cc_start: 0.6856 (OUTLIER) cc_final: 0.6378 (t) REVERT: B 631 GLU cc_start: 0.8261 (tp30) cc_final: 0.8038 (tp30) REVERT: C 336 THR cc_start: 0.9273 (m) cc_final: 0.8972 (p) REVERT: C 570 GLN cc_start: 0.7281 (mm-40) cc_final: 0.5796 (pm20) REVERT: C 631 GLU cc_start: 0.8249 (tp30) cc_final: 0.8033 (tp30) REVERT: D 139 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8101 (tm) REVERT: D 336 THR cc_start: 0.9242 (m) cc_final: 0.8960 (p) REVERT: D 351 MET cc_start: 0.7992 (mtt) cc_final: 0.7776 (mtt) REVERT: D 569 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: D 570 GLN cc_start: 0.7240 (mm-40) cc_final: 0.5763 (pm20) outliers start: 57 outliers final: 41 residues processed: 347 average time/residue: 0.2919 time to fit residues: 161.2342 Evaluate side-chains 334 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 289 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 569 PHE Chi-restraints excluded: chain B residue 582 VAL Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 713 SER Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 548 LEU Chi-restraints excluded: chain C residue 569 PHE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 713 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 124 optimal weight: 0.0870 chunk 166 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 220 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 161 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117766 restraints weight = 81706.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.124370 restraints weight = 38130.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.128718 restraints weight = 24614.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131492 restraints weight = 18825.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133146 restraints weight = 15877.631| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3565 r_free = 0.3565 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22012 Z= 0.140 Angle : 0.621 10.770 29688 Z= 0.318 Chirality : 0.061 1.457 3296 Planarity : 0.005 0.122 3644 Dihedral : 11.795 111.659 3424 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.29 % Favored : 88.56 % Rotamer: Outliers : 2.12 % Allowed : 16.93 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.17), residues: 2552 helix: 1.58 (0.13), residues: 1520 sheet: -2.62 (0.52), residues: 88 loop : -3.48 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 567 TYR 0.012 0.001 TYR C 540 PHE 0.019 0.001 PHE A 316 TRP 0.008 0.001 TRP C 521 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00324 (22004) covalent geometry : angle 0.61984 (29672) SS BOND : bond 0.00302 ( 8) SS BOND : angle 1.39036 ( 16) hydrogen bonds : bond 0.04023 ( 1021) hydrogen bonds : angle 3.97916 ( 3003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 293 time to evaluate : 1.133 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: A 336 THR cc_start: 0.9273 (m) cc_final: 0.8981 (p) REVERT: A 570 GLN cc_start: 0.7087 (mm-40) cc_final: 0.5869 (pm20) REVERT: A 574 MET cc_start: 0.7732 (mtm) cc_final: 0.7433 (mtm) REVERT: B 336 THR cc_start: 0.9260 (m) cc_final: 0.8965 (p) REVERT: B 569 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: B 570 GLN cc_start: 0.7022 (mm-40) cc_final: 0.5767 (pm20) REVERT: B 574 MET cc_start: 0.7687 (mtm) cc_final: 0.7391 (mtm) REVERT: B 631 GLU cc_start: 0.8286 (tp30) cc_final: 0.8063 (tp30) REVERT: C 322 ASP cc_start: 0.8346 (t70) cc_final: 0.7833 (t0) REVERT: C 336 THR cc_start: 0.9276 (m) cc_final: 0.8982 (p) REVERT: C 570 GLN cc_start: 0.7030 (mm-40) cc_final: 0.5802 (pm20) REVERT: C 574 MET cc_start: 0.7707 (mtm) cc_final: 0.7415 (mtm) REVERT: C 631 GLU cc_start: 0.8257 (tp30) cc_final: 0.8030 (tp30) REVERT: D 322 ASP cc_start: 0.8330 (t70) cc_final: 0.7831 (t0) REVERT: D 336 THR cc_start: 0.9262 (m) cc_final: 0.8968 (p) REVERT: D 351 MET cc_start: 0.8064 (mtt) cc_final: 0.7842 (mtt) REVERT: D 569 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: D 570 GLN cc_start: 0.6997 (mm-40) cc_final: 0.5770 (pm20) REVERT: D 574 MET cc_start: 0.7714 (mtm) cc_final: 0.7412 (mtm) outliers start: 48 outliers final: 38 residues processed: 322 average time/residue: 0.2999 time to fit residues: 152.5707 Evaluate side-chains 326 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 286 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 569 PHE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 569 PHE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 588 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 95 optimal weight: 2.9990 chunk 204 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 175 optimal weight: 0.3980 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.161597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118958 restraints weight = 82165.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.125675 restraints weight = 38033.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130094 restraints weight = 24436.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.132881 restraints weight = 18648.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134555 restraints weight = 15716.741| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.134 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.7007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22012 Z= 0.122 Angle : 0.609 10.829 29688 Z= 0.311 Chirality : 0.062 1.482 3296 Planarity : 0.005 0.120 3644 Dihedral : 11.215 104.698 3424 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.85 % Favored : 88.99 % Rotamer: Outliers : 2.07 % Allowed : 17.11 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.17), residues: 2552 helix: 1.75 (0.13), residues: 1520 sheet: -2.59 (0.53), residues: 88 loop : -3.46 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 567 TYR 0.012 0.001 TYR C 540 PHE 0.020 0.001 PHE C 316 TRP 0.008 0.001 TRP C 521 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd covalent geometry : bond 0.00277 (22004) covalent geometry : angle 0.60864 (29672) SS BOND : bond 0.00257 ( 8) SS BOND : angle 1.20363 ( 16) hydrogen bonds : bond 0.03849 ( 1021) hydrogen bonds : angle 3.89138 ( 3003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6672.13 seconds wall clock time: 114 minutes 16.06 seconds (6856.06 seconds total)