Starting phenix.real_space_refine on Tue Jul 7 03:27:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6m_42996/07_2026/8v6m_42996_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6m_42996/07_2026/8v6m_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_42996/07_2026/8v6m_42996_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6m_42996/07_2026/8v6m_42996_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v6m_42996/07_2026/8v6m_42996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6m_42996/07_2026/8v6m_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-dev-6108/lib/python3.11/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, 177 Ad-hoc single atom residues: {' NA': 3} Unusual residues: {'I8E': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 3 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: 6.91, 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: 4.10 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 0.95 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: 9.68 Time building geometry restraints manager: 5.60 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.290 Extract box with map and model: 0.570 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 37.910 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 are 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/Z covalent geometry : bond 0.00599 / 0.29 (22004) covalent geometry : angle 1.06651 / 0.59 (29672) SS BOND : bond 0.00069 / 0.04 ( 8) SS BOND : angle 1.37927 / 0.96 ( 16) hydrogen bonds : bond 0.31947 / 21.57 ( 1021) hydrogen bonds : angle 9.61583 / 6.80 ( 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 : 1.247 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: 0.7731 (m-80) cc_final: 0.7494 (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: 0.4363 time to fit residues: 436.7378 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 : 1.046 ------------------------------------------------------------------------------- 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: 3.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3965 r_free = 0.3965 target = 0.168686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.127882 restraints weight = 80740.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.135354 restraints weight = 34871.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140149 restraints weight = 21510.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.143140 restraints weight = 15983.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.145019 restraints weight = 13229.501| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3692 r_free = 0.3692 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4193 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= 0.192 Angle : 0.778 10.917 29688 Z= 0.407 Chirality : 0.064 1.466 3296 Planarity : 0.005 0.069 3644 Dihedral : 16.168 178.338 3424 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.94 % Allowed : 10.62 % Favored : 88.44 % Rotamer: Outliers : 2.87 % Allowed : 11.07 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.15), residues: 2552 helix: -0.47 (0.12), residues: 1496 sheet: -3.57 (0.43), residues: 76 loop : -3.67 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 698 TYR 0.012 0.001 TYR D 460 PHE 0.015 0.002 PHE C 193 TRP 0.005 0.001 TRP B 692 HIS 0.006 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (22004) covalent geometry : angle 0.77403 / 0.41 (29672) SS BOND : bond 0.00709 / 0.38 ( 8) SS BOND : angle 3.57467 / 2.27 ( 16) hydrogen bonds : bond 0.06522 / 4.41 ( 1021) hydrogen bonds : angle 4.98606 / 3.45 ( 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 444 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 379 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 THR cc_start: 0.9133 (m) cc_final: 0.8636 (p) REVERT: A 555 MET cc_start: 0.7431 (mtm) cc_final: 0.7060 (mtm) REVERT: A 592 PHE cc_start: 0.8019 (t80) cc_final: 0.7780 (t80) REVERT: B 336 THR cc_start: 0.9143 (m) cc_final: 0.8643 (p) REVERT: B 555 MET cc_start: 0.7366 (mtm) cc_final: 0.6991 (mtm) REVERT: B 592 PHE cc_start: 0.7982 (t80) cc_final: 0.7755 (t80) REVERT: C 336 THR cc_start: 0.9125 (m) cc_final: 0.8625 (p) REVERT: C 555 MET cc_start: 0.7412 (mtm) cc_final: 0.7060 (mtm) REVERT: C 592 PHE cc_start: 0.8017 (t80) cc_final: 0.7789 (t80) REVERT: C 677 MET cc_start: 0.7810 (ttp) cc_final: 0.7465 (mmm) REVERT: D 336 THR cc_start: 0.9121 (m) cc_final: 0.8613 (p) REVERT: D 555 MET cc_start: 0.7427 (mtm) cc_final: 0.7076 (mtm) REVERT: D 592 PHE cc_start: 0.8003 (t80) cc_final: 0.7764 (t80) outliers start: 65 outliers final: 48 residues processed: 419 average time/residue: 0.2963 time to fit residues: 198.9488 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 : 1.096 ------------------------------------------------------------------------------- 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: 0.9990 chunk 246 optimal weight: 2.9990 chunk 245 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 202 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3955 r_free = 0.3955 target = 0.167539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.126142 restraints weight = 80423.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.133526 restraints weight = 35120.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138321 restraints weight = 21782.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.141267 restraints weight = 16247.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.143064 restraints weight = 13503.710| |-----------------------------------------------------------------------------| r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22012 Z= 0.149 Angle : 0.693 11.086 29688 Z= 0.359 Chirality : 0.062 1.451 3296 Planarity : 0.004 0.058 3644 Dihedral : 15.192 167.625 3424 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.63 % Allowed : 10.38 % Favored : 88.99 % Rotamer: Outliers : 2.20 % Allowed : 13.36 % Favored : 84.44 % 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 are not related in a simple way. whole: -1.71 (0.16), residues: 2552 helix: 0.44 (0.13), residues: 1524 sheet: -2.95 (0.45), residues: 92 loop : -3.75 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 567 TYR 0.018 0.001 TYR A 460 PHE 0.016 0.001 PHE C 316 TRP 0.007 0.001 TRP C 559 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (22004) covalent geometry : angle 0.68693 / 0.36 (29672) SS BOND : bond 0.01035 / 0.56 ( 8) SS BOND : angle 4.08197 / 2.51 ( 16) hydrogen bonds : bond 0.05302 / 3.58 ( 1021) hydrogen bonds : angle 4.41118 / 3.05 ( 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 373 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 323 time to evaluate : 1.159 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: 0.9145 (m) cc_final: 0.8658 (p) REVERT: A 409 TYR cc_start: 0.7919 (m-80) cc_final: 0.7511 (m-80) REVERT: A 592 PHE cc_start: 0.8057 (t80) cc_final: 0.7856 (t80) REVERT: B 336 THR cc_start: 0.9158 (m) cc_final: 0.8686 (p) REVERT: B 409 TYR cc_start: 0.7887 (m-80) cc_final: 0.7472 (m-80) REVERT: B 592 PHE cc_start: 0.8030 (t80) cc_final: 0.7811 (t80) REVERT: C 336 THR cc_start: 0.9156 (m) cc_final: 0.8665 (p) REVERT: C 409 TYR cc_start: 0.7929 (m-80) cc_final: 0.7514 (m-80) REVERT: C 544 TYR cc_start: 0.7393 (m-80) cc_final: 0.7191 (m-80) REVERT: C 592 PHE cc_start: 0.8043 (t80) cc_final: 0.7836 (t80) REVERT: C 677 MET cc_start: 0.7419 (ttp) cc_final: 0.6709 (mmm) REVERT: D 336 THR cc_start: 0.9138 (m) cc_final: 0.8648 (p) REVERT: D 409 TYR cc_start: 0.7912 (m-80) cc_final: 0.7500 (m-80) outliers start: 50 outliers final: 31 residues processed: 347 average time/residue: 0.2986 time to fit residues: 168.1498 Evaluate side-chains 321 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 290 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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 671 ASN 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 671 ASN 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 513 LEU Chi-restraints excluded: chain C residue 671 ASN 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 513 LEU 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: 2.9990 chunk 142 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 178 ASN A 251 ASN A 401 ASN B 251 ASN B 401 ASN C 251 ASN C 401 ASN D 251 ASN D 401 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.158473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116300 restraints weight = 81874.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.122888 restraints weight = 37851.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127209 restraints weight = 24315.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.129924 restraints weight = 18576.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.131595 restraints weight = 15669.958| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.5763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 22012 Z= 0.228 Angle : 0.728 11.294 29688 Z= 0.383 Chirality : 0.064 1.478 3296 Planarity : 0.005 0.061 3644 Dihedral : 14.710 166.187 3424 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.87 % Favored : 87.66 % Rotamer: Outliers : 3.40 % Allowed : 13.62 % Favored : 82.98 % 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 are not related in a simple way. whole: -1.56 (0.16), residues: 2552 helix: 0.62 (0.13), residues: 1528 sheet: -3.39 (0.48), residues: 88 loop : -3.77 (0.18), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 567 TYR 0.016 0.002 TYR A 451 PHE 0.023 0.002 PHE A 259 TRP 0.012 0.002 TRP D 692 HIS 0.007 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00538 / 0.23 (22004) covalent geometry : angle 0.72409 / 0.38 (29672) SS BOND : bond 0.00308 / 0.17 ( 8) SS BOND : angle 3.15412 / 1.94 ( 16) hydrogen bonds : bond 0.05266 / 3.55 ( 1021) hydrogen bonds : angle 4.51933 / 3.12 ( 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 408 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 331 time to evaluate : 1.182 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 165 SER cc_start: 0.8771 (m) cc_final: 0.8543 (t) REVERT: A 336 THR cc_start: 0.9246 (m) cc_final: 0.8808 (p) REVERT: A 631 GLU cc_start: 0.8387 (tp30) cc_final: 0.8094 (tp30) REVERT: B 165 SER cc_start: 0.8763 (m) cc_final: 0.8543 (t) REVERT: B 336 THR cc_start: 0.9242 (m) cc_final: 0.8802 (p) REVERT: B 545 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7166 (tppt) REVERT: B 592 PHE cc_start: 0.8352 (t80) cc_final: 0.8132 (t80) REVERT: B 631 GLU cc_start: 0.8412 (tp30) cc_final: 0.8130 (tp30) REVERT: B 671 ASN cc_start: 0.7583 (OUTLIER) cc_final: 0.7364 (t160) REVERT: C 165 SER cc_start: 0.8778 (m) cc_final: 0.8561 (t) REVERT: C 336 THR cc_start: 0.9244 (m) cc_final: 0.8806 (p) REVERT: C 592 PHE cc_start: 0.8296 (t80) cc_final: 0.8083 (t80) REVERT: C 631 GLU cc_start: 0.8410 (tp30) cc_final: 0.8125 (tp30) REVERT: C 671 ASN cc_start: 0.7689 (OUTLIER) cc_final: 0.7375 (t0) REVERT: C 677 MET cc_start: 0.7267 (ttp) cc_final: 0.7025 (tmm) REVERT: D 336 THR cc_start: 0.9239 (m) cc_final: 0.8797 (p) REVERT: D 631 GLU cc_start: 0.8398 (tp30) cc_final: 0.8119 (tp30) outliers start: 77 outliers final: 55 residues processed: 382 average time/residue: 0.3115 time to fit residues: 195.2171 Evaluate side-chains 367 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 309 time to evaluate : 1.159 ------------------------------------------------------------------------------- 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 374 SER 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 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 669 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 677 MET 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 374 SER Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 452 ASN 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 545 LYS 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 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 374 SER 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 545 LYS 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 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 374 SER 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 513 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 669 LEU 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: 10.0000 chunk 177 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 238 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 401 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 178 ASN B 401 ASN C 178 ASN C 401 ASN D 178 ASN D 251 ASN D 401 ASN D 671 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.160111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.116811 restraints weight = 81423.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123510 restraints weight = 37943.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.127931 restraints weight = 24536.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130748 restraints weight = 18739.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132462 restraints weight = 15798.251| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3549 r_free = 0.3549 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22012 Z= 0.191 Angle : 0.680 11.307 29688 Z= 0.355 Chirality : 0.062 1.458 3296 Planarity : 0.005 0.110 3644 Dihedral : 14.146 167.375 3424 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.47 % Allowed : 10.82 % Favored : 88.71 % Rotamer: Outliers : 3.70 % Allowed : 13.84 % Favored : 82.45 % 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 are not related in a simple way. whole: -1.40 (0.17), residues: 2552 helix: 0.82 (0.13), residues: 1524 sheet: -3.35 (0.41), residues: 112 loop : -3.82 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 567 TYR 0.013 0.001 TYR C 540 PHE 0.018 0.001 PHE A 316 TRP 0.009 0.001 TRP A 710 HIS 0.003 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (22004) covalent geometry : angle 0.67827 / 0.35 (29672) SS BOND : bond 0.00394 / 0.21 ( 8) SS BOND : angle 2.39120 / 1.48 ( 16) hydrogen bonds : bond 0.04898 / 3.30 ( 1021) hydrogen bonds : angle 4.40338 / 3.04 ( 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 400 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 316 time to evaluate : 1.175 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: A 165 SER cc_start: 0.8727 (m) cc_final: 0.8479 (t) REVERT: A 336 THR cc_start: 0.9243 (m) cc_final: 0.8810 (p) REVERT: A 409 TYR cc_start: 0.7975 (m-80) cc_final: 0.7630 (m-80) REVERT: A 631 GLU cc_start: 0.8426 (tp30) cc_final: 0.8168 (tp30) REVERT: B 165 SER cc_start: 0.8720 (m) cc_final: 0.8473 (t) REVERT: B 336 THR cc_start: 0.9243 (m) cc_final: 0.8808 (p) REVERT: B 545 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7132 (tppt) REVERT: B 631 GLU cc_start: 0.8443 (tp30) cc_final: 0.8188 (tp30) REVERT: C 165 SER cc_start: 0.8735 (m) cc_final: 0.8481 (t) REVERT: C 336 THR cc_start: 0.9243 (m) cc_final: 0.8806 (p) REVERT: C 409 TYR cc_start: 0.7970 (m-80) cc_final: 0.7626 (m-80) REVERT: C 631 GLU cc_start: 0.8421 (tp30) cc_final: 0.8160 (tp30) REVERT: C 671 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7282 (t0) REVERT: D 336 THR cc_start: 0.9247 (m) cc_final: 0.8811 (p) REVERT: D 351 MET cc_start: 0.8137 (mtt) cc_final: 0.7898 (mtt) REVERT: D 409 TYR cc_start: 0.7977 (m-80) cc_final: 0.7708 (m-80) REVERT: D 631 GLU cc_start: 0.8419 (tp30) cc_final: 0.8160 (tp30) outliers start: 84 outliers final: 56 residues processed: 372 average time/residue: 0.3188 time to fit residues: 193.3993 Evaluate side-chains 356 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 298 time to evaluate : 1.073 ------------------------------------------------------------------------------- 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 357 LEU 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 537 VAL Chi-restraints excluded: chain A residue 626 SER 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 357 LEU 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 513 LEU Chi-restraints excluded: chain B residue 545 LYS 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 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 357 LEU 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 626 SER Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain C residue 671 ASN 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 357 LEU Chi-restraints excluded: chain D residue 385 VAL 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 513 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 40 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 236 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 170 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** A 671 ASN ** 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117085 restraints weight = 81197.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123635 restraints weight = 37218.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.127928 restraints weight = 23714.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.130620 restraints weight = 18038.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132382 restraints weight = 15165.429| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 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: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.6353 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= 0.182 Angle : 0.664 11.212 29688 Z= 0.345 Chirality : 0.062 1.450 3296 Planarity : 0.005 0.112 3644 Dihedral : 13.732 164.484 3424 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.31 % Allowed : 11.29 % Favored : 88.40 % Rotamer: Outliers : 4.10 % Allowed : 14.33 % Favored : 81.57 % 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 are not related in a simple way. whole: -1.21 (0.17), residues: 2552 helix: 0.97 (0.13), residues: 1524 sheet: -3.30 (0.41), residues: 112 loop : -3.74 (0.18), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 567 TYR 0.013 0.001 TYR D 540 PHE 0.019 0.001 PHE A 316 TRP 0.010 0.001 TRP B 710 HIS 0.004 0.001 HIS D 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (22004) covalent geometry : angle 0.66186 / 0.34 (29672) SS BOND : bond 0.01010 / 0.55 ( 8) SS BOND : angle 2.24412 / 1.38 ( 16) hydrogen bonds : bond 0.04677 / 3.15 ( 1021) hydrogen bonds : angle 4.30772 / 2.99 ( 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 398 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 305 time to evaluate : 1.134 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: A 336 THR cc_start: 0.9284 (m) cc_final: 0.8939 (p) REVERT: A 631 GLU cc_start: 0.8436 (tp30) cc_final: 0.8170 (tp30) REVERT: A 677 MET cc_start: 0.7583 (ttm) cc_final: 0.7128 (ttp) REVERT: B 336 THR cc_start: 0.9271 (m) cc_final: 0.8929 (p) REVERT: B 631 GLU cc_start: 0.8437 (tp30) cc_final: 0.8187 (tp30) REVERT: C 336 THR cc_start: 0.9282 (m) cc_final: 0.8866 (p) REVERT: C 631 GLU cc_start: 0.8426 (tp30) cc_final: 0.8168 (tp30) REVERT: D 336 THR cc_start: 0.9290 (m) cc_final: 0.8940 (p) REVERT: D 351 MET cc_start: 0.8140 (mtt) cc_final: 0.7908 (mtt) REVERT: D 631 GLU cc_start: 0.8422 (tp30) cc_final: 0.8158 (tp30) REVERT: D 671 ASN cc_start: 0.7780 (t0) cc_final: 0.7396 (t0) outliers start: 93 outliers final: 72 residues processed: 369 average time/residue: 0.3233 time to fit residues: 191.2992 Evaluate side-chains 356 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 284 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 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 357 LEU 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 537 VAL 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 A residue 669 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 176 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 357 LEU 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 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 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 176 LEU 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 357 LEU 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 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 669 LEU Chi-restraints excluded: chain C residue 673 LEU 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 357 LEU Chi-restraints excluded: chain D residue 385 VAL 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 491 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 626 SER Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 673 LEU 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: 6.9990 chunk 157 optimal weight: 4.9990 chunk 201 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 244 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 286 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114050 restraints weight = 81718.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120367 restraints weight = 38010.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.124511 restraints weight = 24536.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127098 restraints weight = 18805.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.128781 restraints weight = 15918.348| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.6637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 22012 Z= 0.210 Angle : 0.682 10.795 29688 Z= 0.356 Chirality : 0.062 1.434 3296 Planarity : 0.005 0.114 3644 Dihedral : 13.607 154.059 3424 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.99 % Favored : 87.85 % Rotamer: Outliers : 4.59 % Allowed : 14.51 % Favored : 80.91 % 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 are not related in a simple way. whole: -1.22 (0.17), residues: 2552 helix: 0.99 (0.13), residues: 1520 sheet: -3.28 (0.40), residues: 112 loop : -3.77 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 567 TYR 0.014 0.002 TYR C 451 PHE 0.018 0.001 PHE C 316 TRP 0.009 0.001 TRP A 521 HIS 0.004 0.001 HIS B 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.21 (22004) covalent geometry : angle 0.67991 / 0.36 (29672) SS BOND : bond 0.00359 / 0.19 ( 8) SS BOND : angle 2.19025 / 1.35 ( 16) hydrogen bonds : bond 0.04873 / 3.28 ( 1021) hydrogen bonds : angle 4.37840 / 3.03 ( 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 406 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 302 time to evaluate : 1.154 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: A 159 MET cc_start: 0.7276 (mmm) cc_final: 0.7027 (mmm) REVERT: A 322 ASP cc_start: 0.8442 (t70) cc_final: 0.7899 (t0) REVERT: A 631 GLU cc_start: 0.8389 (tp30) cc_final: 0.8172 (tp30) REVERT: B 322 ASP cc_start: 0.8487 (t70) cc_final: 0.7895 (t0) REVERT: B 336 THR cc_start: 0.9317 (m) cc_final: 0.8979 (p) REVERT: B 545 LYS cc_start: 0.7640 (pptt) cc_final: 0.7088 (tppt) REVERT: B 631 GLU cc_start: 0.8409 (tp30) cc_final: 0.8187 (tp30) REVERT: C 322 ASP cc_start: 0.8489 (t70) cc_final: 0.7915 (t0) REVERT: C 631 GLU cc_start: 0.8401 (tp30) cc_final: 0.8181 (tp30) REVERT: D 322 ASP cc_start: 0.8542 (t70) cc_final: 0.7923 (t0) REVERT: D 336 THR cc_start: 0.9324 (m) cc_final: 0.9000 (p) REVERT: D 351 MET cc_start: 0.8173 (mtt) cc_final: 0.7942 (mtt) REVERT: D 631 GLU cc_start: 0.8377 (tp30) cc_final: 0.8158 (tp30) outliers start: 104 outliers final: 87 residues processed: 369 average time/residue: 0.3241 time to fit residues: 192.3966 Evaluate side-chains 374 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 287 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 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 357 LEU Chi-restraints excluded: chain A residue 374 SER 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 537 VAL 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 A residue 669 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 677 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 176 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 357 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 401 ASN 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 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 648 SER Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 176 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 357 LEU Chi-restraints excluded: chain C residue 374 SER Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 401 ASN 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 491 LEU 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 648 SER Chi-restraints excluded: chain C residue 669 LEU 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 357 LEU Chi-restraints excluded: chain D residue 374 SER Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 401 ASN 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 491 LEU Chi-restraints excluded: chain D residue 498 SER 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 626 SER Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 28 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 189 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 149 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** 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 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.156438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.113720 restraints weight = 82753.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.120174 restraints weight = 39097.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.124394 restraints weight = 25396.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.127056 restraints weight = 19545.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128730 restraints weight = 16580.114| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.6781 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= 0.183 Angle : 0.664 11.057 29688 Z= 0.344 Chirality : 0.062 1.440 3296 Planarity : 0.005 0.120 3644 Dihedral : 13.280 143.330 3424 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.99 % Favored : 87.85 % Rotamer: Outliers : 4.23 % Allowed : 15.12 % Favored : 80.64 % 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 are not related in a simple way. whole: -1.12 (0.17), residues: 2552 helix: 1.07 (0.13), residues: 1520 sheet: -3.24 (0.40), residues: 112 loop : -3.73 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 567 TYR 0.013 0.001 TYR A 540 PHE 0.018 0.001 PHE A 316 TRP 0.009 0.001 TRP A 710 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.18 (22004) covalent geometry : angle 0.66230 / 0.34 (29672) SS BOND : bond 0.00404 / 0.22 ( 8) SS BOND : angle 1.87956 / 1.15 ( 16) hydrogen bonds : bond 0.04685 / 3.15 ( 1021) hydrogen bonds : angle 4.30125 / 2.97 ( 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 383 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 287 time to evaluate : 1.194 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: A 322 ASP cc_start: 0.8444 (t70) cc_final: 0.7906 (t0) REVERT: A 336 THR cc_start: 0.9317 (m) cc_final: 0.9001 (p) REVERT: A 631 GLU cc_start: 0.8393 (tp30) cc_final: 0.8183 (tp30) REVERT: B 322 ASP cc_start: 0.8451 (t70) cc_final: 0.7899 (t0) REVERT: B 336 THR cc_start: 0.9315 (m) cc_final: 0.8981 (p) REVERT: B 631 GLU cc_start: 0.8414 (tp30) cc_final: 0.8195 (tp30) REVERT: C 322 ASP cc_start: 0.8458 (t70) cc_final: 0.7909 (t0) REVERT: C 336 THR cc_start: 0.9313 (m) cc_final: 0.8996 (p) REVERT: C 631 GLU cc_start: 0.8388 (tp30) cc_final: 0.8173 (tp30) REVERT: D 322 ASP cc_start: 0.8543 (t70) cc_final: 0.7895 (t0) REVERT: D 336 THR cc_start: 0.9314 (m) cc_final: 0.8996 (p) REVERT: D 351 MET cc_start: 0.8153 (mtt) cc_final: 0.7918 (mtt) REVERT: D 631 GLU cc_start: 0.8384 (tp30) cc_final: 0.8163 (tp30) REVERT: D 671 ASN cc_start: 0.7780 (t0) cc_final: 0.7385 (t0) outliers start: 96 outliers final: 82 residues processed: 357 average time/residue: 0.3303 time to fit residues: 190.5323 Evaluate side-chains 364 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 282 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 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 357 LEU Chi-restraints excluded: chain A residue 374 SER 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 537 VAL 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 A residue 669 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 176 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 357 LEU Chi-restraints excluded: chain B residue 374 SER 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 588 LEU Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain C residue 176 LEU 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 357 LEU Chi-restraints excluded: chain C residue 374 SER 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 491 LEU 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 648 SER Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 176 LEU 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 357 LEU Chi-restraints excluded: chain D residue 385 VAL 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 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 626 SER Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 187 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 203 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 225 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** 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 = 0.3883 r_free = 0.3883 target = 0.160687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.118910 restraints weight = 80823.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.125492 restraints weight = 37537.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.129813 restraints weight = 24107.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132498 restraints weight = 18372.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134258 restraints weight = 15481.709| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.6901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22012 Z= 0.125 Angle : 0.625 10.932 29688 Z= 0.319 Chirality : 0.061 1.457 3296 Planarity : 0.005 0.118 3644 Dihedral : 12.292 120.446 3424 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.05 % Favored : 88.79 % Rotamer: Outliers : 3.04 % Allowed : 16.14 % 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 are not related in a simple way. whole: -0.74 (0.17), residues: 2552 helix: 1.39 (0.13), residues: 1520 sheet: -3.08 (0.43), residues: 112 loop : -3.60 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 693 TYR 0.013 0.001 TYR B 540 PHE 0.020 0.001 PHE C 316 TRP 0.009 0.001 TRP A 739 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (22004) covalent geometry : angle 0.62421 / 0.32 (29672) SS BOND : bond 0.00363 / 0.19 ( 8) SS BOND : angle 1.41094 / 0.86 ( 16) hydrogen bonds : bond 0.04134 / 2.78 ( 1021) hydrogen bonds : angle 4.04450 / 2.79 ( 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 364 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 295 time to evaluate : 1.179 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: A 322 ASP cc_start: 0.8360 (t70) cc_final: 0.7813 (t0) REVERT: A 336 THR cc_start: 0.9308 (m) cc_final: 0.9017 (p) REVERT: A 631 GLU cc_start: 0.8290 (tp30) cc_final: 0.8064 (tp30) REVERT: B 322 ASP cc_start: 0.8358 (t70) cc_final: 0.7844 (t0) REVERT: B 336 THR cc_start: 0.9293 (m) cc_final: 0.8994 (p) REVERT: B 631 GLU cc_start: 0.8298 (tp30) cc_final: 0.8075 (tp30) REVERT: C 322 ASP cc_start: 0.8368 (t70) cc_final: 0.7817 (t0) REVERT: C 336 THR cc_start: 0.9301 (m) cc_final: 0.9010 (p) REVERT: C 631 GLU cc_start: 0.8284 (tp30) cc_final: 0.8069 (tp30) REVERT: D 322 ASP cc_start: 0.8458 (t70) cc_final: 0.7856 (t70) REVERT: D 336 THR cc_start: 0.9303 (m) cc_final: 0.9004 (p) REVERT: D 351 MET cc_start: 0.8017 (mtt) cc_final: 0.7791 (mtt) REVERT: D 631 GLU cc_start: 0.8286 (tp30) cc_final: 0.8060 (tp30) outliers start: 69 outliers final: 62 residues processed: 342 average time/residue: 0.3342 time to fit residues: 183.4384 Evaluate side-chains 344 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 282 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 LEU 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 357 LEU 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 537 VAL 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 673 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 177 LEU 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 357 LEU 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 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 C residue 176 LEU 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 357 LEU 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 551 LEU Chi-restraints excluded: chain C residue 569 PHE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 177 LEU 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 357 LEU 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 669 LEU Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 131 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 166 optimal weight: 10.0000 chunk 128 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 286 GLN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.155891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113400 restraints weight = 82833.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119782 restraints weight = 39469.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123955 restraints weight = 25747.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.126588 restraints weight = 19880.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.128250 restraints weight = 16892.748| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22012 Z= 0.209 Angle : 0.678 10.795 29688 Z= 0.351 Chirality : 0.062 1.450 3296 Planarity : 0.006 0.126 3644 Dihedral : 12.554 112.885 3424 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.91 % Favored : 87.93 % Rotamer: Outliers : 3.09 % Allowed : 16.14 % Favored : 80.78 % 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 are not related in a simple way. whole: -0.94 (0.17), residues: 2552 helix: 1.21 (0.13), residues: 1520 sheet: -2.90 (0.50), residues: 88 loop : -3.69 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 567 TYR 0.014 0.001 TYR C 451 PHE 0.018 0.001 PHE C 316 TRP 0.009 0.001 TRP A 521 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (22004) covalent geometry : angle 0.67707 / 0.35 (29672) SS BOND : bond 0.00392 / 0.21 ( 8) SS BOND : angle 1.72983 / 1.06 ( 16) hydrogen bonds : bond 0.04649 / 3.13 ( 1021) hydrogen bonds : angle 4.29274 / 2.97 ( 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 348 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 278 time to evaluate : 1.157 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: A 322 ASP cc_start: 0.8482 (t70) cc_final: 0.7901 (t0) REVERT: A 336 THR cc_start: 0.9332 (m) cc_final: 0.9031 (p) REVERT: A 570 GLN cc_start: 0.7197 (mm-40) cc_final: 0.5866 (pm20) REVERT: A 574 MET cc_start: 0.7813 (mtm) cc_final: 0.7527 (mtm) REVERT: A 631 GLU cc_start: 0.8368 (tp30) cc_final: 0.8161 (tp30) REVERT: B 173 MET cc_start: 0.8096 (ttm) cc_final: 0.7860 (ttm) REVERT: B 322 ASP cc_start: 0.8504 (t70) cc_final: 0.7909 (t0) REVERT: B 336 THR cc_start: 0.9323 (m) cc_final: 0.9014 (p) REVERT: B 631 GLU cc_start: 0.8391 (tp30) cc_final: 0.8188 (tp30) REVERT: C 322 ASP cc_start: 0.8486 (t70) cc_final: 0.7895 (t0) REVERT: C 336 THR cc_start: 0.9335 (m) cc_final: 0.9032 (p) REVERT: C 570 GLN cc_start: 0.7226 (mm-40) cc_final: 0.5850 (pm20) REVERT: C 574 MET cc_start: 0.7827 (mtm) cc_final: 0.7536 (mtm) REVERT: C 631 GLU cc_start: 0.8393 (tp30) cc_final: 0.8179 (tp30) REVERT: D 173 MET cc_start: 0.8095 (ttm) cc_final: 0.7869 (ttm) REVERT: D 322 ASP cc_start: 0.8590 (t70) cc_final: 0.7934 (t0) REVERT: D 336 THR cc_start: 0.9329 (m) cc_final: 0.9021 (p) REVERT: D 351 MET cc_start: 0.8141 (mtt) cc_final: 0.7908 (mtt) REVERT: D 631 GLU cc_start: 0.8382 (tp30) cc_final: 0.8173 (tp30) outliers start: 70 outliers final: 58 residues processed: 327 average time/residue: 0.3399 time to fit residues: 177.2412 Evaluate side-chains 333 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 275 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 357 LEU 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 537 VAL 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 673 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 357 LEU 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 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 C residue 176 LEU Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 357 LEU 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 491 LEU 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 669 LEU Chi-restraints excluded: chain D residue 176 LEU 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 357 LEU 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 669 LEU Chi-restraints excluded: chain D residue 673 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: 9.9990 chunk 30 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 44 optimal weight: 0.0270 chunk 19 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 251 ASN ** 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 = 0.3875 r_free = 0.3875 target = 0.160193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118449 restraints weight = 81476.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.125004 restraints weight = 37933.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.129332 restraints weight = 24373.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.132041 restraints weight = 18586.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133797 restraints weight = 15650.102| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3552 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3552 r_free = 0.3552 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3552 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.7109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22012 Z= 0.125 Angle : 0.631 10.886 29688 Z= 0.321 Chirality : 0.062 1.462 3296 Planarity : 0.005 0.121 3644 Dihedral : 12.049 107.312 3424 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.93 % Favored : 88.91 % Rotamer: Outliers : 2.65 % Allowed : 16.84 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.17), residues: 2552 helix: 1.45 (0.13), residues: 1520 sheet: -2.98 (0.43), residues: 112 loop : -3.58 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 693 TYR 0.013 0.001 TYR A 540 PHE 0.021 0.001 PHE C 316 TRP 0.008 0.001 TRP B 739 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (22004) covalent geometry : angle 0.63006 / 0.32 (29672) SS BOND : bond 0.00289 / 0.15 ( 8) SS BOND : angle 1.33189 / 0.82 ( 16) hydrogen bonds : bond 0.04168 / 2.79 ( 1021) hydrogen bonds : angle 4.02349 / 2.78 ( 3003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7335.54 seconds wall clock time: 125 minutes 48.67 seconds (7548.67 seconds total)