Starting phenix.real_space_refine on Thu Dec 26 04:07:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v6m_42996/12_2024/8v6m_42996_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v6m_42996/12_2024/8v6m_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8v6m_42996/12_2024/8v6m_42996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v6m_42996/12_2024/8v6m_42996.map" model { file = "/net/cci-nas-00/data/ceres_data/8v6m_42996/12_2024/8v6m_42996_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v6m_42996/12_2024/8v6m_42996_trim.cif" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 42639 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10482 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "B" Number of atoms: 10482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10482 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "C" Number of atoms: 10482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10482 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "D" Number of atoms: 10482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 640, 10482 Classifications: {'peptide': 640} Link IDs: {'PTRANS': 17, 'TRANS': 622} Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 180 Unusual residues: {' NA': 3, 'I8E': 1, 'POV': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'I8E': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'I8E': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'I8E': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 20.05, per 1000 atoms: 0.47 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: 12.19 Conformation dependent library (CDL) restraints added in 3.3 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: 3.67 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: 16.36 Time building geometry restraints manager: 14.05 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 756 or resid 901 through 902)) selection = (chain 'B' and (resid 117 through 756 or resid 901 through 902)) selection = (chain 'C' and (resid 117 through 756 or resid 901 through 902)) selection = (chain 'D' and (resid 117 through 756 or resid 901 through 902)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.750 Extract box with map and model: 1.620 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 87.080 Find NCS groups from input model: 1.970 Set up NCS constraints: 0.190 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: 0.020 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 22004 Z= 0.387 Angle : 1.067 11.317 29672 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP B 331 HIS 0.007 0.001 HIS B 523 PHE 0.016 0.002 PHE A 316 TYR 0.016 0.001 TYR C 564 ARG 0.006 0.001 ARG C 464 *********************** 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 : 3.363 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: 0.8008 (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: 0.8107 (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: 0.7540 (m-80) REVERT: C 282 MET cc_start: 0.8940 (tpp) cc_final: 0.8051 (tpt) REVERT: C 336 THR cc_start: 0.9202 (m) cc_final: 0.8825 (p) REVERT: C 409 TYR cc_start: 0.7732 (m-80) cc_final: 0.7494 (m-80) REVERT: D 282 MET cc_start: 0.9053 (tpp) cc_final: 0.8174 (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: 0.7438 (m-80) outliers start: 0 outliers final: 0 residues processed: 700 average time/residue: 1.0100 time to fit residues: 1009.6207 Evaluate side-chains 370 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 3.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 103 optimal weight: 10.0000 chunk 200 optimal weight: 8.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 149 optimal weight: 4.9990 chunk 232 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 ASN A 227 GLN A 242 ASN A 251 ASN A 401 ASN A 452 ASN A 647 ASN A 735 ASN B 205 ASN B 227 GLN B 242 ASN B 251 ASN B 401 ASN B 452 ASN B 647 ASN B 735 ASN C 205 ASN C 227 GLN C 242 ASN C 251 ASN C 401 ASN C 452 ASN C 647 ASN C 735 ASN D 205 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: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22004 Z= 0.349 Angle : 0.804 10.949 29672 Z= 0.422 Chirality : 0.065 1.482 3296 Planarity : 0.005 0.067 3644 Dihedral : 16.319 179.435 3424 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.94 % Allowed : 11.09 % Favored : 87.97 % Rotamer: Outliers : 2.87 % Allowed : 11.02 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.15), residues: 2552 helix: -0.62 (0.12), residues: 1528 sheet: -3.34 (0.46), residues: 68 loop : -3.83 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 692 HIS 0.008 0.001 HIS A 301 PHE 0.016 0.002 PHE C 259 TYR 0.015 0.002 TYR D 460 ARG 0.008 0.001 ARG D 567 *********************** 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 442 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 377 time to evaluate : 3.468 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: A 336 THR cc_start: 0.9286 (m) cc_final: 0.8912 (p) REVERT: A 409 TYR cc_start: 0.8049 (m-80) cc_final: 0.7615 (m-80) REVERT: B 336 THR cc_start: 0.9289 (m) cc_final: 0.8918 (p) REVERT: B 409 TYR cc_start: 0.8036 (m-80) cc_final: 0.7673 (m-80) REVERT: C 336 THR cc_start: 0.9292 (m) cc_final: 0.8942 (p) REVERT: C 409 TYR cc_start: 0.8053 (m-80) cc_final: 0.7618 (m-80) REVERT: D 336 THR cc_start: 0.9247 (m) cc_final: 0.8805 (p) REVERT: D 409 TYR cc_start: 0.8038 (m-80) cc_final: 0.7641 (m-80) outliers start: 65 outliers final: 45 residues processed: 417 average time/residue: 0.7433 time to fit residues: 492.3811 Evaluate side-chains 326 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 3.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 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 648 SER Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 671 ASN 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 129 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 158 optimal weight: 0.4980 chunk 64 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 251 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 230 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 401 ASN C 401 ASN D 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22004 Z= 0.214 Angle : 0.681 11.106 29672 Z= 0.352 Chirality : 0.061 1.447 3296 Planarity : 0.004 0.060 3644 Dihedral : 15.212 165.369 3424 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.63 % Allowed : 9.95 % Favored : 89.42 % Rotamer: Outliers : 2.56 % Allowed : 12.48 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.48 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.17), residues: 2552 helix: 0.50 (0.13), residues: 1532 sheet: -2.99 (0.44), residues: 92 loop : -3.72 (0.19), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 559 HIS 0.003 0.001 HIS A 471 PHE 0.017 0.001 PHE B 316 TYR 0.016 0.001 TYR D 460 ARG 0.004 0.000 ARG C 567 *********************** 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 371 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 313 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 THR cc_start: 0.9306 (m) cc_final: 0.8962 (p) REVERT: A 409 TYR cc_start: 0.7999 (m-80) cc_final: 0.7727 (m-80) REVERT: A 592 PHE cc_start: 0.8238 (t80) cc_final: 0.8035 (t80) REVERT: B 336 THR cc_start: 0.9305 (m) cc_final: 0.8960 (p) REVERT: B 409 TYR cc_start: 0.7994 (m-80) cc_final: 0.7719 (m-80) REVERT: B 592 PHE cc_start: 0.8231 (t80) cc_final: 0.8019 (t80) REVERT: C 336 THR cc_start: 0.9302 (m) cc_final: 0.8980 (p) REVERT: C 409 TYR cc_start: 0.7993 (m-80) cc_final: 0.7724 (m-80) REVERT: C 592 PHE cc_start: 0.8230 (t80) cc_final: 0.8021 (t80) REVERT: D 336 THR cc_start: 0.9264 (m) cc_final: 0.8857 (p) REVERT: D 409 TYR cc_start: 0.7973 (m-80) cc_final: 0.7671 (m-80) outliers start: 58 outliers final: 33 residues processed: 345 average time/residue: 0.6778 time to fit residues: 375.9401 Evaluate side-chains 314 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 281 time to evaluate : 3.285 ------------------------------------------------------------------------------- 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 459 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 459 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 498 SER 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 414 ASP Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 498 SER 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 230 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 233 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 66 optimal weight: 20.0000 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN A 251 ASN A 401 ASN B 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22004 Z= 0.240 Angle : 0.662 11.246 29672 Z= 0.344 Chirality : 0.061 1.461 3296 Planarity : 0.004 0.056 3644 Dihedral : 14.275 167.525 3424 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.47 % Allowed : 11.44 % Favored : 88.09 % Rotamer: Outliers : 3.04 % Allowed : 13.40 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.17), residues: 2552 helix: 0.89 (0.13), residues: 1524 sheet: -3.60 (0.39), residues: 112 loop : -3.71 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 559 HIS 0.004 0.001 HIS C 301 PHE 0.016 0.002 PHE C 193 TYR 0.013 0.001 TYR C 540 ARG 0.005 0.000 ARG A 567 *********************** 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 385 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 316 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 SER cc_start: 0.8701 (m) cc_final: 0.8451 (t) REVERT: A 336 THR cc_start: 0.9306 (m) cc_final: 0.8998 (p) REVERT: A 409 TYR cc_start: 0.8000 (m-80) cc_final: 0.7737 (m-80) REVERT: A 631 GLU cc_start: 0.8379 (tp30) cc_final: 0.8167 (tp30) REVERT: B 336 THR cc_start: 0.9306 (m) cc_final: 0.9005 (p) REVERT: B 409 TYR cc_start: 0.7978 (m-80) cc_final: 0.7716 (m-80) REVERT: B 545 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7177 (tppt) REVERT: C 165 SER cc_start: 0.8683 (m) cc_final: 0.8434 (t) REVERT: C 336 THR cc_start: 0.9299 (m) cc_final: 0.9016 (p) REVERT: C 409 TYR cc_start: 0.7985 (m-80) cc_final: 0.7728 (m-80) REVERT: D 336 THR cc_start: 0.9275 (m) cc_final: 0.8907 (p) REVERT: D 409 TYR cc_start: 0.7978 (m-80) cc_final: 0.7683 (m-80) REVERT: D 631 GLU cc_start: 0.8388 (tp30) cc_final: 0.8172 (tp30) outliers start: 69 outliers final: 49 residues processed: 355 average time/residue: 0.6793 time to fit residues: 389.4427 Evaluate side-chains 347 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 297 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 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 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 498 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 673 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 513 LEU 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 414 ASP Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 459 SER Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 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 206 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 184 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 211 optimal weight: 0.3980 chunk 171 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 222 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN C 401 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22004 Z= 0.332 Angle : 0.697 10.977 29672 Z= 0.366 Chirality : 0.062 1.447 3296 Planarity : 0.005 0.101 3644 Dihedral : 14.143 167.858 3424 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.13 % Favored : 88.52 % Rotamer: Outliers : 3.66 % Allowed : 13.67 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.17), residues: 2552 helix: 0.84 (0.13), residues: 1528 sheet: -3.41 (0.40), residues: 112 loop : -3.77 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 692 HIS 0.005 0.001 HIS C 301 PHE 0.020 0.002 PHE C 569 TYR 0.013 0.002 TYR A 451 ARG 0.005 0.000 ARG D 567 *********************** 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 406 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 323 time to evaluate : 3.596 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 165 SER cc_start: 0.8642 (m) cc_final: 0.8354 (t) REVERT: A 336 THR cc_start: 0.9348 (m) cc_final: 0.9044 (p) REVERT: A 631 GLU cc_start: 0.8500 (tp30) cc_final: 0.8256 (tp30) REVERT: A 671 ASN cc_start: 0.7430 (t0) cc_final: 0.7077 (t0) REVERT: B 165 SER cc_start: 0.8623 (m) cc_final: 0.8342 (t) REVERT: B 336 THR cc_start: 0.9352 (m) cc_final: 0.9052 (p) REVERT: B 555 MET cc_start: 0.7450 (mtm) cc_final: 0.7198 (mtm) REVERT: B 592 PHE cc_start: 0.8504 (t80) cc_final: 0.8304 (t80) REVERT: C 165 SER cc_start: 0.8615 (m) cc_final: 0.8314 (t) REVERT: C 336 THR cc_start: 0.9344 (m) cc_final: 0.9059 (p) REVERT: C 592 PHE cc_start: 0.8511 (t80) cc_final: 0.8292 (t80) REVERT: D 336 THR cc_start: 0.9328 (m) cc_final: 0.8961 (p) REVERT: D 351 MET cc_start: 0.8218 (mtt) cc_final: 0.7993 (mtt) REVERT: D 631 GLU cc_start: 0.8494 (tp30) cc_final: 0.8235 (tp30) outliers start: 83 outliers final: 54 residues processed: 380 average time/residue: 0.6797 time to fit residues: 417.5767 Evaluate side-chains 358 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 304 time to evaluate : 3.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 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 588 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 414 ASP Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain C residue 669 LEU Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 264 THR Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 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 544 TYR Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 669 LEU Chi-restraints excluded: chain D residue 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 0.8980 chunk 222 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 247 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 130 optimal weight: 20.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN C 286 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22004 Z= 0.259 Angle : 0.647 11.144 29672 Z= 0.337 Chirality : 0.062 1.448 3296 Planarity : 0.005 0.112 3644 Dihedral : 13.647 164.033 3424 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.68 % Favored : 88.17 % Rotamer: Outliers : 3.31 % Allowed : 15.08 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.17), residues: 2552 helix: 0.98 (0.13), residues: 1528 sheet: -3.32 (0.41), residues: 112 loop : -3.69 (0.18), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 710 HIS 0.004 0.001 HIS C 256 PHE 0.020 0.001 PHE A 316 TYR 0.014 0.001 TYR C 540 ARG 0.004 0.000 ARG D 567 *********************** 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 375 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 300 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 THR cc_start: 0.9367 (m) cc_final: 0.9094 (p) REVERT: A 631 GLU cc_start: 0.8435 (tp30) cc_final: 0.8224 (tp30) REVERT: A 671 ASN cc_start: 0.7458 (t0) cc_final: 0.7104 (t0) REVERT: B 336 THR cc_start: 0.9350 (m) cc_final: 0.9077 (p) REVERT: C 336 THR cc_start: 0.9364 (m) cc_final: 0.9101 (p) REVERT: D 336 THR cc_start: 0.9346 (m) cc_final: 0.8994 (p) REVERT: D 351 MET cc_start: 0.8189 (mtt) cc_final: 0.7964 (mtt) REVERT: D 631 GLU cc_start: 0.8451 (tp30) cc_final: 0.8217 (tp30) outliers start: 75 outliers final: 62 residues processed: 344 average time/residue: 0.7352 time to fit residues: 400.8113 Evaluate side-chains 352 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 290 time to evaluate : 3.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 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 677 MET Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 462 ARG Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 569 PHE Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 626 SER Chi-restraints excluded: chain C residue 648 SER Chi-restraints excluded: chain C residue 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 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 462 ARG 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 542 PHE Chi-restraints excluded: chain D residue 544 TYR 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 180 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 208 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 246 optimal weight: 1.9990 chunk 154 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 286 GLN ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN A 671 ASN B 286 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** B 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 286 GLN ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.6663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22004 Z= 0.228 Angle : 0.635 10.911 29672 Z= 0.328 Chirality : 0.061 1.444 3296 Planarity : 0.005 0.112 3644 Dihedral : 13.173 151.565 3424 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.48 % Favored : 88.36 % Rotamer: Outliers : 3.35 % Allowed : 15.12 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.17), residues: 2552 helix: 1.17 (0.13), residues: 1520 sheet: -3.17 (0.42), residues: 112 loop : -3.65 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 710 HIS 0.004 0.001 HIS D 256 PHE 0.019 0.001 PHE D 316 TYR 0.014 0.001 TYR C 540 ARG 0.004 0.000 ARG B 567 *********************** 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 374 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 298 time to evaluate : 3.463 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 671 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.7021 (t0) REVERT: B 336 THR cc_start: 0.9374 (m) cc_final: 0.9165 (p) REVERT: B 570 GLN cc_start: 0.6915 (mm-40) cc_final: 0.6051 (pm20) REVERT: C 159 MET cc_start: 0.7248 (mmm) cc_final: 0.7016 (mmm) REVERT: C 570 GLN cc_start: 0.6853 (mm-40) cc_final: 0.6055 (pm20) REVERT: D 336 THR cc_start: 0.9355 (m) cc_final: 0.9090 (p) REVERT: D 351 MET cc_start: 0.8152 (mtt) cc_final: 0.7931 (mtt) REVERT: D 570 GLN cc_start: 0.6942 (mm-40) cc_final: 0.5916 (pm20) outliers start: 76 outliers final: 58 residues processed: 346 average time/residue: 0.7532 time to fit residues: 407.1658 Evaluate side-chains 345 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 286 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 456 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 498 SER Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 456 THR Chi-restraints excluded: chain B residue 462 ARG Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 569 PHE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 648 SER Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 498 SER Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain C residue 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 385 VAL Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 456 THR Chi-restraints excluded: chain D residue 498 SER Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 147 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 48 optimal weight: 0.3980 chunk 47 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 193 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 ASN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 ASN ** C 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22004 Z= 0.184 Angle : 0.618 10.804 29672 Z= 0.317 Chirality : 0.061 1.454 3296 Planarity : 0.005 0.116 3644 Dihedral : 12.601 137.913 3424 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.60 % Favored : 88.24 % Rotamer: Outliers : 2.60 % Allowed : 15.65 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2552 helix: 1.34 (0.13), residues: 1520 sheet: -3.08 (0.42), residues: 112 loop : -3.54 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 739 HIS 0.004 0.001 HIS C 256 PHE 0.019 0.001 PHE A 316 TYR 0.013 0.001 TYR D 540 ARG 0.006 0.000 ARG A 462 *********************** 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 359 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 300 time to evaluate : 3.155 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: A 545 LYS cc_start: 0.7558 (pptt) cc_final: 0.7223 (tptt) REVERT: A 570 GLN cc_start: 0.7225 (mm-40) cc_final: 0.6210 (pm20) REVERT: A 574 MET cc_start: 0.7877 (mtm) cc_final: 0.7645 (mtm) REVERT: B 570 GLN cc_start: 0.6587 (mm-40) cc_final: 0.6108 (pm20) REVERT: C 139 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7729 (tm) REVERT: C 570 GLN cc_start: 0.6597 (mm-40) cc_final: 0.6178 (pm20) REVERT: C 574 MET cc_start: 0.7758 (mtm) cc_final: 0.7485 (mtm) REVERT: D 336 THR cc_start: 0.9347 (m) cc_final: 0.9091 (p) REVERT: D 351 MET cc_start: 0.8085 (mtt) cc_final: 0.7864 (mtt) REVERT: D 570 GLN cc_start: 0.6720 (mm-40) cc_final: 0.6050 (pm20) outliers start: 59 outliers final: 51 residues processed: 336 average time/residue: 0.7636 time to fit residues: 415.8702 Evaluate side-chains 339 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 287 time to evaluate : 3.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 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 385 VAL Chi-restraints excluded: chain B residue 401 ASN Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain B residue 569 PHE Chi-restraints excluded: chain B residue 588 LEU Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 139 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 385 VAL Chi-restraints excluded: chain C residue 401 ASN Chi-restraints excluded: chain C residue 421 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 648 SER Chi-restraints excluded: chain C residue 669 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 385 VAL Chi-restraints excluded: chain D residue 401 ASN Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 0.4980 chunk 236 optimal weight: 0.8980 chunk 215 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 207 optimal weight: 0.8980 chunk 217 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** B 313 GLN ** 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22004 Z= 0.184 Angle : 0.618 11.065 29672 Z= 0.316 Chirality : 0.061 1.464 3296 Planarity : 0.005 0.119 3644 Dihedral : 12.258 127.889 3424 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.21 % Favored : 88.64 % Rotamer: Outliers : 2.29 % Allowed : 15.78 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.17), residues: 2552 helix: 1.43 (0.13), residues: 1520 sheet: -3.03 (0.43), residues: 112 loop : -3.51 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 710 HIS 0.004 0.001 HIS C 256 PHE 0.018 0.001 PHE C 316 TYR 0.013 0.001 TYR D 540 ARG 0.003 0.000 ARG D 567 *********************** 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 350 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 298 time to evaluate : 3.372 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: A 545 LYS cc_start: 0.7554 (pptt) cc_final: 0.7194 (tptt) REVERT: A 570 GLN cc_start: 0.7033 (mm-40) cc_final: 0.6213 (pm20) REVERT: A 574 MET cc_start: 0.7885 (mtm) cc_final: 0.7644 (mtm) REVERT: B 322 ASP cc_start: 0.8302 (t70) cc_final: 0.7812 (t70) REVERT: B 570 GLN cc_start: 0.6476 (mm-40) cc_final: 0.6008 (pm20) REVERT: B 574 MET cc_start: 0.7774 (mtm) cc_final: 0.7500 (mtm) REVERT: C 570 GLN cc_start: 0.6438 (mm-40) cc_final: 0.6131 (pm20) REVERT: C 574 MET cc_start: 0.7767 (mtm) cc_final: 0.7502 (mtm) REVERT: D 336 THR cc_start: 0.9329 (m) cc_final: 0.9093 (p) REVERT: D 351 MET cc_start: 0.8091 (mtt) cc_final: 0.7865 (mtt) REVERT: D 570 GLN cc_start: 0.6535 (mm-40) cc_final: 0.5872 (pm20) REVERT: D 574 MET cc_start: 0.7747 (mtm) cc_final: 0.7441 (mtm) outliers start: 52 outliers final: 50 residues processed: 327 average time/residue: 0.7488 time to fit residues: 388.2961 Evaluate side-chains 340 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 290 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 145 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 385 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 462 ARG 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 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 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 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 385 VAL Chi-restraints excluded: chain D residue 421 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 chunk 255 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 203 optimal weight: 10.0000 chunk 21 optimal weight: 0.0980 chunk 156 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 401 ASN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.7023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22004 Z= 0.229 Angle : 0.637 11.178 29672 Z= 0.326 Chirality : 0.061 1.472 3296 Planarity : 0.005 0.122 3644 Dihedral : 12.065 112.896 3424 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.40 % Favored : 88.44 % Rotamer: Outliers : 2.43 % Allowed : 16.14 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.17), residues: 2552 helix: 1.41 (0.13), residues: 1520 sheet: -2.70 (0.52), residues: 88 loop : -3.57 (0.18), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 521 HIS 0.004 0.001 HIS C 256 PHE 0.019 0.001 PHE B 316 TYR 0.012 0.001 TYR D 540 ARG 0.004 0.000 ARG D 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5104 Ramachandran restraints generated. 2552 Oldfield, 0 Emsley, 2552 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 286 time to evaluate : 3.600 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: A 322 ASP cc_start: 0.8342 (t70) cc_final: 0.7852 (t70) REVERT: A 570 GLN cc_start: 0.6787 (mm-40) cc_final: 0.6262 (pm20) REVERT: A 574 MET cc_start: 0.7816 (mtm) cc_final: 0.7483 (mtm) REVERT: B 322 ASP cc_start: 0.8352 (t70) cc_final: 0.7831 (t0) REVERT: B 570 GLN cc_start: 0.6335 (mm-40) cc_final: 0.6020 (pm20) REVERT: B 574 MET cc_start: 0.7769 (mtm) cc_final: 0.7488 (mtt) REVERT: C 322 ASP cc_start: 0.8312 (t70) cc_final: 0.7842 (t70) REVERT: C 570 GLN cc_start: 0.6333 (mm-40) cc_final: 0.6087 (pm20) REVERT: C 574 MET cc_start: 0.7743 (mtm) cc_final: 0.7467 (mtt) REVERT: D 322 ASP cc_start: 0.8403 (t70) cc_final: 0.7857 (t70) REVERT: D 336 THR cc_start: 0.9360 (m) cc_final: 0.9104 (p) REVERT: D 351 MET cc_start: 0.8126 (mtt) cc_final: 0.7905 (mtt) REVERT: D 570 GLN cc_start: 0.6442 (mm-40) cc_final: 0.5946 (pm20) REVERT: D 574 MET cc_start: 0.7749 (mtm) cc_final: 0.7444 (mtt) outliers start: 55 outliers final: 46 residues processed: 320 average time/residue: 0.7401 time to fit residues: 371.0386 Evaluate side-chains 326 residues out of total 2268 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 280 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 312 THR Chi-restraints excluded: chain A residue 385 VAL Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 569 PHE Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 626 SER Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 462 ARG 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 648 SER Chi-restraints excluded: chain B residue 669 LEU Chi-restraints excluded: chain B residue 677 MET Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 385 VAL Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 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 677 MET Chi-restraints excluded: chain D residue 207 GLU Chi-restraints excluded: chain D residue 312 THR Chi-restraints excluded: chain D residue 385 VAL Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 491 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain D residue 569 PHE Chi-restraints excluded: chain D residue 588 LEU Chi-restraints excluded: chain D residue 648 SER Chi-restraints excluded: chain D residue 669 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 0.0060 chunk 62 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 203 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 208 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 178 optimal weight: 10.0000 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.160489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118139 restraints weight = 82268.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124883 restraints weight = 38219.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129228 restraints weight = 24640.671| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.7115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22004 Z= 0.185 Angle : 0.622 10.831 29672 Z= 0.316 Chirality : 0.062 1.469 3296 Planarity : 0.005 0.120 3644 Dihedral : 11.544 106.733 3424 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.09 % Favored : 88.75 % Rotamer: Outliers : 2.12 % Allowed : 16.23 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2552 helix: 1.57 (0.13), residues: 1520 sheet: -2.96 (0.44), residues: 112 loop : -3.49 (0.18), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 521 HIS 0.004 0.001 HIS C 256 PHE 0.020 0.001 PHE A 316 TYR 0.012 0.001 TYR D 540 ARG 0.003 0.000 ARG D 567 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9170.02 seconds wall clock time: 165 minutes 2.79 seconds (9902.79 seconds total)