Starting phenix.real_space_refine on Sat Sep 28 19:30:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/09_2024/8can_16531.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/09_2024/8can_16531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/09_2024/8can_16531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/09_2024/8can_16531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/09_2024/8can_16531.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8can_16531/09_2024/8can_16531.cif" } resolution = 1.93 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= 0.000 sd= 0.010 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 Cu 24 5.60 5 S 396 5.16 5 Na 3 4.78 5 C 21840 2.51 5 N 5754 2.21 5 O 9278 1.98 5 H 33930 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 71225 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "B" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "C" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "D" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "E" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "F" Number of atoms: 11314 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 683, 11275 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 656} Chain breaks: 3 bond proxies already assigned to first conformer: 11367 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CU': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CU': 4, ' NA': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' CU': 4, ' NA': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Unusual residues: {' CU': 4} Inner-chain residues flagged as termini: ['pdbres="TRP D 801 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 29 Unusual residues: {' CU': 4, ' NA': 1} Inner-chain residues flagged as termini: ['pdbres="TRP E 801 "'] Classifications: {'peptide': 1, 'undetermined': 5} Modifications used: {'COO': 1} Link IDs: {None: 5} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 28 Unusual residues: {' CU': 4} Inner-chain residues flagged as termini: ['pdbres="TRP F 801 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Chain: "A" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 525 Classifications: {'water': 525} Link IDs: {None: 524} Chain: "B" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 520 Classifications: {'water': 520} Link IDs: {None: 519} Chain: "C" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 540, 540 Classifications: {'water': 540} Link IDs: {None: 539} Chain: "D" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 529 Classifications: {'water': 529} Link IDs: {None: 528} Chain: "E" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 523 Classifications: {'water': 523} Link IDs: {None: 522} Chain: "F" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 533 Classifications: {'water': 533} Link IDs: {None: 532} Time building chain proxies: 44.36, per 1000 atoms: 0.62 Number of scatterers: 71225 At special positions: 0 Unit cell: (137.896, 134.632, 113.417, 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) Cu 24 28.99 S 396 16.00 Na 3 11.00 O 9278 8.00 N 5754 7.00 C 21840 6.00 H 33930 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 293 " - pdb=" SG CYS A 544 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 293 " - pdb=" SG CYS B 544 " distance=2.03 Simple disulfide: pdb=" SG CYS B 663 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 544 " distance=2.03 Simple disulfide: pdb=" SG CYS C 663 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 544 " distance=2.03 Simple disulfide: pdb=" SG CYS D 663 " - pdb=" SG CYS D 668 " distance=2.03 Simple disulfide: pdb=" SG CYS E 293 " - pdb=" SG CYS E 544 " distance=2.03 Simple disulfide: pdb=" SG CYS E 663 " - pdb=" SG CYS E 668 " distance=2.03 Simple disulfide: pdb=" SG CYS F 293 " - pdb=" SG CYS F 544 " distance=2.03 Simple disulfide: pdb=" SG CYS F 663 " - pdb=" SG CYS F 668 " 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: 13.18 Conformation dependent library (CDL) restraints added in 7.3 seconds 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7884 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 36 sheets defined 44.9% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.46 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 Processing helix chain 'A' and resid 76 through 80 Processing helix chain 'A' and resid 82 through 96 removed outlier: 3.777A pdb=" N VAL A 86 " --> pdb=" O LYS A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 124 Processing helix chain 'A' and resid 127 through 140 removed outlier: 3.875A pdb=" N GLU A 140 " --> pdb=" O CYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 158 Processing helix chain 'A' and resid 159 through 162 removed outlier: 3.788A pdb=" N SER A 162 " --> pdb=" O SER A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 159 through 162' Processing helix chain 'A' and resid 168 through 173 Processing helix chain 'A' and resid 174 through 177 Processing helix chain 'A' and resid 179 through 193 Processing helix chain 'A' and resid 197 through 205 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 232 through 237 Processing helix chain 'A' and resid 238 through 252 Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 267 through 290 removed outlier: 3.542A pdb=" N HIS A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 355 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 372 through 382 Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 420 through 424 removed outlier: 3.544A pdb=" N MET A 424 " --> pdb=" O ALA A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 430 Processing helix chain 'A' and resid 431 through 452 removed outlier: 3.563A pdb=" N TRP A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU A 443 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 461 Processing helix chain 'A' and resid 487 through 490 Processing helix chain 'A' and resid 493 through 500 Processing helix chain 'A' and resid 550 through 555 Processing helix chain 'A' and resid 556 through 558 No H-bonds generated for 'chain 'A' and resid 556 through 558' Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' Processing helix chain 'A' and resid 609 through 617 removed outlier: 4.172A pdb=" N ARG A 615 " --> pdb=" O TRP A 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 616 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 661 removed outlier: 3.867A pdb=" N ALA A 657 " --> pdb=" O ASP A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 709 removed outlier: 3.784A pdb=" N ASN A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET A 709 " --> pdb=" O ALA A 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 704 through 709' Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.824A pdb=" N LYS A 730 " --> pdb=" O TYR A 727 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP A 731 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 Processing helix chain 'B' and resid 76 through 80 Processing helix chain 'B' and resid 82 through 96 removed outlier: 3.777A pdb=" N VAL B 86 " --> pdb=" O LYS B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 124 Processing helix chain 'B' and resid 127 through 140 removed outlier: 3.876A pdb=" N GLU B 140 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 158 Processing helix chain 'B' and resid 159 through 162 removed outlier: 3.788A pdb=" N SER B 162 " --> pdb=" O SER B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 159 through 162' Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 174 through 177 Processing helix chain 'B' and resid 179 through 193 Processing helix chain 'B' and resid 197 through 205 Processing helix chain 'B' and resid 227 through 231 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 238 through 252 Processing helix chain 'B' and resid 261 through 266 Processing helix chain 'B' and resid 267 through 290 removed outlier: 3.541A pdb=" N HIS B 290 " --> pdb=" O GLU B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 355 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 420 through 424 removed outlier: 3.544A pdb=" N MET B 424 " --> pdb=" O ALA B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 430 Processing helix chain 'B' and resid 431 through 452 removed outlier: 3.563A pdb=" N TRP B 435 " --> pdb=" O ASP B 431 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU B 443 " --> pdb=" O LYS B 439 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 461 Processing helix chain 'B' and resid 487 through 490 Processing helix chain 'B' and resid 493 through 500 Processing helix chain 'B' and resid 550 through 555 Processing helix chain 'B' and resid 556 through 558 No H-bonds generated for 'chain 'B' and resid 556 through 558' Processing helix chain 'B' and resid 580 through 582 No H-bonds generated for 'chain 'B' and resid 580 through 582' Processing helix chain 'B' and resid 609 through 617 removed outlier: 4.172A pdb=" N ARG B 615 " --> pdb=" O TRP B 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 616 " --> pdb=" O TYR B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 661 removed outlier: 3.867A pdb=" N ALA B 657 " --> pdb=" O ASP B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 709 removed outlier: 3.785A pdb=" N ASN B 708 " --> pdb=" O LEU B 704 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET B 709 " --> pdb=" O ALA B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 709' Processing helix chain 'B' and resid 726 through 731 removed outlier: 3.824A pdb=" N LYS B 730 " --> pdb=" O TYR B 727 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP B 731 " --> pdb=" O LEU B 728 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 52 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 82 through 96 removed outlier: 3.777A pdb=" N VAL C 86 " --> pdb=" O LYS C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 124 Processing helix chain 'C' and resid 127 through 140 removed outlier: 3.875A pdb=" N GLU C 140 " --> pdb=" O CYS C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 158 Processing helix chain 'C' and resid 159 through 162 removed outlier: 3.788A pdb=" N SER C 162 " --> pdb=" O SER C 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 159 through 162' Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 174 through 177 Processing helix chain 'C' and resid 179 through 193 Processing helix chain 'C' and resid 197 through 205 Processing helix chain 'C' and resid 227 through 231 Processing helix chain 'C' and resid 232 through 237 Processing helix chain 'C' and resid 238 through 252 Processing helix chain 'C' and resid 261 through 266 Processing helix chain 'C' and resid 267 through 290 removed outlier: 3.541A pdb=" N HIS C 290 " --> pdb=" O GLU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 355 Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 372 through 382 Processing helix chain 'C' and resid 400 through 405 Processing helix chain 'C' and resid 420 through 424 removed outlier: 3.543A pdb=" N MET C 424 " --> pdb=" O ALA C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 430 Processing helix chain 'C' and resid 431 through 452 removed outlier: 3.563A pdb=" N TRP C 435 " --> pdb=" O ASP C 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU C 443 " --> pdb=" O LYS C 439 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE C 445 " --> pdb=" O ILE C 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 456 through 461 Processing helix chain 'C' and resid 487 through 490 Processing helix chain 'C' and resid 493 through 500 Processing helix chain 'C' and resid 550 through 555 Processing helix chain 'C' and resid 556 through 558 No H-bonds generated for 'chain 'C' and resid 556 through 558' Processing helix chain 'C' and resid 580 through 582 No H-bonds generated for 'chain 'C' and resid 580 through 582' Processing helix chain 'C' and resid 609 through 617 removed outlier: 4.173A pdb=" N ARG C 615 " --> pdb=" O TRP C 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 616 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 661 removed outlier: 3.867A pdb=" N ALA C 657 " --> pdb=" O ASP C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 709 removed outlier: 3.785A pdb=" N ASN C 708 " --> pdb=" O LEU C 704 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET C 709 " --> pdb=" O ALA C 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 704 through 709' Processing helix chain 'C' and resid 726 through 731 removed outlier: 3.825A pdb=" N LYS C 730 " --> pdb=" O TYR C 727 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP C 731 " --> pdb=" O LEU C 728 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 52 Processing helix chain 'D' and resid 76 through 80 Processing helix chain 'D' and resid 82 through 96 removed outlier: 3.778A pdb=" N VAL D 86 " --> pdb=" O LYS D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 124 Processing helix chain 'D' and resid 127 through 140 removed outlier: 3.876A pdb=" N GLU D 140 " --> pdb=" O CYS D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 158 Processing helix chain 'D' and resid 159 through 162 removed outlier: 3.787A pdb=" N SER D 162 " --> pdb=" O SER D 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 159 through 162' Processing helix chain 'D' and resid 168 through 173 Processing helix chain 'D' and resid 174 through 177 Processing helix chain 'D' and resid 179 through 193 Processing helix chain 'D' and resid 197 through 205 Processing helix chain 'D' and resid 227 through 231 Processing helix chain 'D' and resid 232 through 237 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 261 through 266 Processing helix chain 'D' and resid 267 through 290 removed outlier: 3.542A pdb=" N HIS D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 355 Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 372 through 382 Processing helix chain 'D' and resid 400 through 405 Processing helix chain 'D' and resid 420 through 424 removed outlier: 3.544A pdb=" N MET D 424 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 430 Processing helix chain 'D' and resid 431 through 452 removed outlier: 3.563A pdb=" N TRP D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLU D 443 " --> pdb=" O LYS D 439 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR D 444 " --> pdb=" O LEU D 440 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE D 445 " --> pdb=" O ILE D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 456 through 461 Processing helix chain 'D' and resid 487 through 490 Processing helix chain 'D' and resid 493 through 500 Processing helix chain 'D' and resid 550 through 555 Processing helix chain 'D' and resid 556 through 558 No H-bonds generated for 'chain 'D' and resid 556 through 558' Processing helix chain 'D' and resid 580 through 582 No H-bonds generated for 'chain 'D' and resid 580 through 582' Processing helix chain 'D' and resid 609 through 617 removed outlier: 4.172A pdb=" N ARG D 615 " --> pdb=" O TRP D 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE D 616 " --> pdb=" O TYR D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 653 through 661 removed outlier: 3.867A pdb=" N ALA D 657 " --> pdb=" O ASP D 653 " (cutoff:3.500A) Processing helix chain 'D' and resid 704 through 709 removed outlier: 3.785A pdb=" N ASN D 708 " --> pdb=" O LEU D 704 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET D 709 " --> pdb=" O ALA D 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 704 through 709' Processing helix chain 'D' and resid 726 through 731 removed outlier: 3.824A pdb=" N LYS D 730 " --> pdb=" O TYR D 727 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP D 731 " --> pdb=" O LEU D 728 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 52 Processing helix chain 'E' and resid 76 through 80 Processing helix chain 'E' and resid 82 through 96 removed outlier: 3.777A pdb=" N VAL E 86 " --> pdb=" O LYS E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 124 Processing helix chain 'E' and resid 127 through 140 removed outlier: 3.875A pdb=" N GLU E 140 " --> pdb=" O CYS E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 158 Processing helix chain 'E' and resid 159 through 162 removed outlier: 3.788A pdb=" N SER E 162 " --> pdb=" O SER E 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 159 through 162' Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'E' and resid 174 through 177 Processing helix chain 'E' and resid 179 through 193 Processing helix chain 'E' and resid 197 through 205 Processing helix chain 'E' and resid 227 through 231 Processing helix chain 'E' and resid 232 through 237 Processing helix chain 'E' and resid 238 through 252 Processing helix chain 'E' and resid 261 through 266 Processing helix chain 'E' and resid 267 through 290 removed outlier: 3.542A pdb=" N HIS E 290 " --> pdb=" O GLU E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 355 Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 372 through 382 Processing helix chain 'E' and resid 400 through 405 Processing helix chain 'E' and resid 420 through 424 removed outlier: 3.543A pdb=" N MET E 424 " --> pdb=" O ALA E 421 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 430 Processing helix chain 'E' and resid 431 through 452 removed outlier: 3.564A pdb=" N TRP E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU E 443 " --> pdb=" O LYS E 439 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR E 444 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N PHE E 445 " --> pdb=" O ILE E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 461 Processing helix chain 'E' and resid 487 through 490 Processing helix chain 'E' and resid 493 through 500 Processing helix chain 'E' and resid 550 through 555 Processing helix chain 'E' and resid 556 through 558 No H-bonds generated for 'chain 'E' and resid 556 through 558' Processing helix chain 'E' and resid 580 through 582 No H-bonds generated for 'chain 'E' and resid 580 through 582' Processing helix chain 'E' and resid 609 through 617 removed outlier: 4.172A pdb=" N ARG E 615 " --> pdb=" O TRP E 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE E 616 " --> pdb=" O TYR E 612 " (cutoff:3.500A) Processing helix chain 'E' and resid 653 through 661 removed outlier: 3.866A pdb=" N ALA E 657 " --> pdb=" O ASP E 653 " (cutoff:3.500A) Processing helix chain 'E' and resid 704 through 709 removed outlier: 3.784A pdb=" N ASN E 708 " --> pdb=" O LEU E 704 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET E 709 " --> pdb=" O ALA E 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 704 through 709' Processing helix chain 'E' and resid 726 through 731 removed outlier: 3.824A pdb=" N LYS E 730 " --> pdb=" O TYR E 727 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP E 731 " --> pdb=" O LEU E 728 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 52 Processing helix chain 'F' and resid 76 through 80 Processing helix chain 'F' and resid 82 through 96 removed outlier: 3.777A pdb=" N VAL F 86 " --> pdb=" O LYS F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 Processing helix chain 'F' and resid 127 through 140 removed outlier: 3.875A pdb=" N GLU F 140 " --> pdb=" O CYS F 136 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 158 Processing helix chain 'F' and resid 159 through 162 removed outlier: 3.787A pdb=" N SER F 162 " --> pdb=" O SER F 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 159 through 162' Processing helix chain 'F' and resid 168 through 173 Processing helix chain 'F' and resid 174 through 177 Processing helix chain 'F' and resid 179 through 193 Processing helix chain 'F' and resid 197 through 205 Processing helix chain 'F' and resid 227 through 231 Processing helix chain 'F' and resid 232 through 237 Processing helix chain 'F' and resid 238 through 252 Processing helix chain 'F' and resid 261 through 266 Processing helix chain 'F' and resid 267 through 290 removed outlier: 3.542A pdb=" N HIS F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 334 through 355 Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 372 through 382 Processing helix chain 'F' and resid 400 through 405 Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.543A pdb=" N MET F 424 " --> pdb=" O ALA F 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 430 Processing helix chain 'F' and resid 431 through 452 removed outlier: 3.563A pdb=" N TRP F 435 " --> pdb=" O ASP F 431 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU F 443 " --> pdb=" O LYS F 439 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N TYR F 444 " --> pdb=" O LEU F 440 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N PHE F 445 " --> pdb=" O ILE F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 456 through 461 Processing helix chain 'F' and resid 487 through 490 Processing helix chain 'F' and resid 493 through 500 Processing helix chain 'F' and resid 550 through 555 Processing helix chain 'F' and resid 556 through 558 No H-bonds generated for 'chain 'F' and resid 556 through 558' Processing helix chain 'F' and resid 580 through 582 No H-bonds generated for 'chain 'F' and resid 580 through 582' Processing helix chain 'F' and resid 609 through 617 removed outlier: 4.172A pdb=" N ARG F 615 " --> pdb=" O TRP F 611 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE F 616 " --> pdb=" O TYR F 612 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 661 removed outlier: 3.867A pdb=" N ALA F 657 " --> pdb=" O ASP F 653 " (cutoff:3.500A) Processing helix chain 'F' and resid 704 through 709 removed outlier: 3.784A pdb=" N ASN F 708 " --> pdb=" O LEU F 704 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N MET F 709 " --> pdb=" O ALA F 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 704 through 709' Processing helix chain 'F' and resid 726 through 731 removed outlier: 3.824A pdb=" N LYS F 730 " --> pdb=" O TYR F 727 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASP F 731 " --> pdb=" O LEU F 728 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 206 through 209 removed outlier: 3.817A pdb=" N HIS A 511 " --> pdb=" O TRP A 218 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 475 " --> pdb=" O TYR A 700 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL A 530 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS A 567 " --> pdb=" O VAL A 530 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N CYS A 532 " --> pdb=" O LEU A 565 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU A 565 " --> pdb=" O CYS A 532 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL A 534 " --> pdb=" O SER A 563 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 563 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL A 536 " --> pdb=" O ILE A 561 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 303 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA4, first strand: chain 'A' and resid 465 through 472 removed outlier: 6.575A pdb=" N ASP A 523 " --> pdb=" O GLU A 468 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL A 470 " --> pdb=" O THR A 521 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR A 521 " --> pdb=" O VAL A 470 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR A 472 " --> pdb=" O LYS A 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS A 519 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 585 through 586 Processing sheet with id=AA6, first strand: chain 'A' and resid 719 through 720 Processing sheet with id=AA7, first strand: chain 'B' and resid 206 through 209 removed outlier: 3.817A pdb=" N HIS B 511 " --> pdb=" O TRP B 218 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU B 475 " --> pdb=" O TYR B 700 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 530 " --> pdb=" O LYS B 567 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS B 567 " --> pdb=" O VAL B 530 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS B 532 " --> pdb=" O LEU B 565 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU B 565 " --> pdb=" O CYS B 532 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL B 534 " --> pdb=" O SER B 563 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 563 " --> pdb=" O VAL B 534 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 536 " --> pdb=" O ILE B 561 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 303 through 304 Processing sheet with id=AA9, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AB1, first strand: chain 'B' and resid 465 through 472 removed outlier: 6.576A pdb=" N ASP B 523 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL B 470 " --> pdb=" O THR B 521 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR B 521 " --> pdb=" O VAL B 470 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B 472 " --> pdb=" O LYS B 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS B 519 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 585 through 586 Processing sheet with id=AB3, first strand: chain 'B' and resid 719 through 720 Processing sheet with id=AB4, first strand: chain 'C' and resid 206 through 209 removed outlier: 3.816A pdb=" N HIS C 511 " --> pdb=" O TRP C 218 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 475 " --> pdb=" O TYR C 700 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL C 530 " --> pdb=" O LYS C 567 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS C 567 " --> pdb=" O VAL C 530 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS C 532 " --> pdb=" O LEU C 565 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU C 565 " --> pdb=" O CYS C 532 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL C 534 " --> pdb=" O SER C 563 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER C 563 " --> pdb=" O VAL C 534 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 536 " --> pdb=" O ILE C 561 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 303 through 304 Processing sheet with id=AB6, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AB7, first strand: chain 'C' and resid 465 through 472 removed outlier: 6.576A pdb=" N ASP C 523 " --> pdb=" O GLU C 468 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL C 470 " --> pdb=" O THR C 521 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR C 521 " --> pdb=" O VAL C 470 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR C 472 " --> pdb=" O LYS C 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS C 519 " --> pdb=" O THR C 472 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 585 through 586 Processing sheet with id=AB9, first strand: chain 'C' and resid 719 through 720 Processing sheet with id=AC1, first strand: chain 'D' and resid 206 through 209 removed outlier: 3.817A pdb=" N HIS D 511 " --> pdb=" O TRP D 218 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU D 475 " --> pdb=" O TYR D 700 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL D 530 " --> pdb=" O LYS D 567 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LYS D 567 " --> pdb=" O VAL D 530 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS D 532 " --> pdb=" O LEU D 565 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU D 565 " --> pdb=" O CYS D 532 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL D 534 " --> pdb=" O SER D 563 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER D 563 " --> pdb=" O VAL D 534 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 536 " --> pdb=" O ILE D 561 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 303 through 304 Processing sheet with id=AC3, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AC4, first strand: chain 'D' and resid 465 through 472 removed outlier: 6.576A pdb=" N ASP D 523 " --> pdb=" O GLU D 468 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL D 470 " --> pdb=" O THR D 521 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR D 521 " --> pdb=" O VAL D 470 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR D 472 " --> pdb=" O LYS D 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS D 519 " --> pdb=" O THR D 472 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 585 through 586 Processing sheet with id=AC6, first strand: chain 'D' and resid 719 through 720 Processing sheet with id=AC7, first strand: chain 'E' and resid 206 through 209 removed outlier: 3.817A pdb=" N HIS E 511 " --> pdb=" O TRP E 218 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU E 475 " --> pdb=" O TYR E 700 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL E 530 " --> pdb=" O LYS E 567 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS E 567 " --> pdb=" O VAL E 530 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N CYS E 532 " --> pdb=" O LEU E 565 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LEU E 565 " --> pdb=" O CYS E 532 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL E 534 " --> pdb=" O SER E 563 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER E 563 " --> pdb=" O VAL E 534 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL E 536 " --> pdb=" O ILE E 561 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 303 through 304 Processing sheet with id=AC9, first strand: chain 'E' and resid 356 through 358 Processing sheet with id=AD1, first strand: chain 'E' and resid 465 through 472 removed outlier: 6.575A pdb=" N ASP E 523 " --> pdb=" O GLU E 468 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL E 470 " --> pdb=" O THR E 521 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR E 521 " --> pdb=" O VAL E 470 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR E 472 " --> pdb=" O LYS E 519 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS E 519 " --> pdb=" O THR E 472 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 585 through 586 Processing sheet with id=AD3, first strand: chain 'E' and resid 719 through 720 Processing sheet with id=AD4, first strand: chain 'F' and resid 206 through 209 removed outlier: 3.817A pdb=" N HIS F 511 " --> pdb=" O TRP F 218 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU F 475 " --> pdb=" O TYR F 700 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL F 530 " --> pdb=" O LYS F 567 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS F 567 " --> pdb=" O VAL F 530 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N CYS F 532 " --> pdb=" O LEU F 565 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU F 565 " --> pdb=" O CYS F 532 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL F 534 " --> pdb=" O SER F 563 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER F 563 " --> pdb=" O VAL F 534 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL F 536 " --> pdb=" O ILE F 561 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 303 through 304 Processing sheet with id=AD6, first strand: chain 'F' and resid 356 through 358 Processing sheet with id=AD7, first strand: chain 'F' and resid 465 through 472 removed outlier: 6.576A pdb=" N ASP F 523 " --> pdb=" O GLU F 468 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N VAL F 470 " --> pdb=" O THR F 521 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N THR F 521 " --> pdb=" O VAL F 470 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR F 472 " --> pdb=" O LYS F 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS F 519 " --> pdb=" O THR F 472 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 585 through 586 Processing sheet with id=AD9, first strand: chain 'F' and resid 719 through 720 1356 hydrogen bonds defined for protein. 3684 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: 29.15 Time building geometry restraints manager: 16.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 33900 1.03 - 1.23: 30 1.23 - 1.42: 14640 1.42 - 1.62: 19548 1.62 - 1.81: 738 Bond restraints: 68856 Sorted by residual: bond pdb=" CA MET A 97 " pdb=" C MET A 97 " ideal model delta sigma weight residual 1.523 1.531 -0.007 1.34e-02 5.57e+03 3.07e-01 bond pdb=" CA MET C 97 " pdb=" C MET C 97 " ideal model delta sigma weight residual 1.523 1.531 -0.007 1.34e-02 5.57e+03 2.97e-01 bond pdb=" C LYS C 110 " pdb=" O LYS C 110 " ideal model delta sigma weight residual 1.236 1.242 -0.006 1.15e-02 7.56e+03 2.46e-01 bond pdb=" C MET E 272 " pdb=" O MET E 272 " ideal model delta sigma weight residual 1.236 1.242 -0.006 1.15e-02 7.56e+03 2.41e-01 bond pdb=" C LYS F 110 " pdb=" O LYS F 110 " ideal model delta sigma weight residual 1.236 1.242 -0.006 1.15e-02 7.56e+03 2.39e-01 ... (remaining 68851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.76: 110823 0.76 - 1.53: 12607 1.53 - 2.29: 878 2.29 - 3.06: 54 3.06 - 3.82: 108 Bond angle restraints: 124470 Sorted by residual: angle pdb=" C ILE F 616 " pdb=" CA ILE F 616 " pdb=" CB ILE F 616 " ideal model delta sigma weight residual 112.36 110.47 1.89 1.37e+00 5.33e-01 1.89e+00 angle pdb=" C ILE B 616 " pdb=" CA ILE B 616 " pdb=" CB ILE B 616 " ideal model delta sigma weight residual 112.36 110.48 1.88 1.37e+00 5.33e-01 1.89e+00 angle pdb=" C LYS E 209 " pdb=" N ASP E 210 " pdb=" CA ASP E 210 " ideal model delta sigma weight residual 123.05 125.21 -2.16 1.57e+00 4.06e-01 1.89e+00 angle pdb=" C LYS D 209 " pdb=" N ASP D 210 " pdb=" CA ASP D 210 " ideal model delta sigma weight residual 123.05 125.20 -2.15 1.57e+00 4.06e-01 1.87e+00 angle pdb=" C ILE D 616 " pdb=" CA ILE D 616 " pdb=" CB ILE D 616 " ideal model delta sigma weight residual 112.36 110.49 1.87 1.37e+00 5.33e-01 1.86e+00 ... (remaining 124465 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.61: 30797 15.61 - 31.23: 1069 31.23 - 46.84: 342 46.84 - 62.45: 120 62.45 - 78.06: 18 Dihedral angle restraints: 32346 sinusoidal: 17520 harmonic: 14826 Sorted by residual: dihedral pdb=" N MET F 46 " pdb=" CA MET F 46 " pdb=" CB MET F 46 " pdb=" CG MET F 46 " ideal model delta sinusoidal sigma weight residual -180.00 -131.44 -48.56 3 1.50e+01 4.44e-03 8.66e+00 dihedral pdb=" N MET B 46 " pdb=" CA MET B 46 " pdb=" CB MET B 46 " pdb=" CG MET B 46 " ideal model delta sinusoidal sigma weight residual -180.00 -131.45 -48.55 3 1.50e+01 4.44e-03 8.65e+00 dihedral pdb=" N MET D 46 " pdb=" CA MET D 46 " pdb=" CB MET D 46 " pdb=" CG MET D 46 " ideal model delta sinusoidal sigma weight residual -180.00 -131.48 -48.52 3 1.50e+01 4.44e-03 8.65e+00 ... (remaining 32343 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 3345 0.029 - 0.058: 1108 0.058 - 0.087: 206 0.087 - 0.116: 244 0.116 - 0.146: 65 Chirality restraints: 4968 Sorted by residual: chirality pdb=" CA ILE B 418 " pdb=" N ILE B 418 " pdb=" C ILE B 418 " pdb=" CB ILE B 418 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE C 418 " pdb=" N ILE C 418 " pdb=" C ILE C 418 " pdb=" CB ILE C 418 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.27e-01 chirality pdb=" CA ILE A 418 " pdb=" N ILE A 418 " pdb=" C ILE A 418 " pdb=" CB ILE A 418 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 4965 not shown) Planarity restraints: 9840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE E 676 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO E 677 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 677 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 677 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 676 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO C 677 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 677 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 677 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE D 676 " -0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO D 677 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO D 677 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 677 " -0.014 5.00e-02 4.00e+02 ... (remaining 9837 not shown) Histogram of nonbonded interaction distances: 1.31 - 1.97: 362 1.97 - 2.63: 84664 2.63 - 3.29: 220576 3.29 - 3.94: 293239 3.94 - 4.60: 461306 Nonbonded interactions: 1060147 Sorted by model distance: nonbonded pdb="HD22 ASN F 573 " pdb=" O HOH F 903 " model vdw 1.315 2.450 nonbonded pdb="HD22 ASN C 573 " pdb=" O HOH C 903 " model vdw 1.332 2.450 nonbonded pdb=" H THR B 420 " pdb=" OD2 ASP B 423 " model vdw 1.626 2.450 nonbonded pdb=" H THR C 420 " pdb=" OD2 ASP C 423 " model vdw 1.626 2.450 nonbonded pdb=" H THR F 420 " pdb=" OD2 ASP F 423 " model vdw 1.626 2.450 ... (remaining 1060142 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 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 803 through 804)) selection = (chain 'B' and (resid 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 803 through 804)) selection = (chain 'C' and (resid 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 803 through 804)) selection = (chain 'D' and (resid 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 802 through 803)) selection = (chain 'E' and (resid 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 803 through 804)) selection = (chain 'F' and (resid 34 through 102 or resid 104 through 111 or resid 113 throu \ gh 639 or resid 641 through 739 or resid 802 through 803)) } 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=0.23 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.270 Extract box with map and model: 2.060 Check model and map are aligned: 0.430 Set scattering table: 0.500 Process input model: 141.440 Find NCS groups from input model: 3.340 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 162.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 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 : 0.002 0.015 34926 Z= 0.099 Angle : 0.399 3.821 47022 Z= 0.219 Chirality : 0.038 0.146 4968 Planarity : 0.003 0.028 5904 Dihedral : 9.004 78.063 13386 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.16 % Allowed : 1.43 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.63 (0.14), residues: 4068 helix: 1.26 (0.14), residues: 1446 sheet: 0.38 (0.21), residues: 606 loop : 1.44 (0.15), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 273 HIS 0.003 0.001 HIS D 54 PHE 0.011 0.001 PHE D 537 TYR 0.011 0.001 TYR F 149 ARG 0.002 0.000 ARG A 398 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 828 time to evaluate : 4.263 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 36 MET cc_start: 0.1390 (ttt) cc_final: 0.1149 (ttp) REVERT: A 78 ASP cc_start: 0.6046 (p0) cc_final: 0.5728 (p0) REVERT: B 36 MET cc_start: 0.1134 (ttt) cc_final: 0.0926 (ttp) REVERT: B 50 LYS cc_start: 0.7853 (mttt) cc_final: 0.7637 (mtmt) REVERT: B 72 VAL cc_start: 0.6258 (t) cc_final: 0.5968 (m) REVERT: B 226 MET cc_start: 0.8782 (mmm) cc_final: 0.8535 (mmm) REVERT: B 292 MET cc_start: 0.8549 (mtm) cc_final: 0.8344 (mtp) REVERT: B 732 MET cc_start: 0.7944 (mmp) cc_final: 0.7723 (mmp) REVERT: C 36 MET cc_start: 0.1530 (ttt) cc_final: 0.1251 (ttp) REVERT: C 129 ASP cc_start: 0.6769 (t70) cc_final: 0.6548 (t0) REVERT: C 213 MET cc_start: 0.7758 (ttm) cc_final: 0.7367 (ttp) REVERT: C 320 MET cc_start: 0.9072 (mtt) cc_final: 0.8862 (mtt) REVERT: C 363 THR cc_start: 0.7861 (p) cc_final: 0.7571 (m) REVERT: C 732 MET cc_start: 0.7991 (mmp) cc_final: 0.7755 (mmp) REVERT: D 36 MET cc_start: 0.1374 (ttt) cc_final: 0.1135 (ttp) REVERT: D 78 ASP cc_start: 0.6048 (p0) cc_final: 0.5719 (p0) REVERT: E 36 MET cc_start: 0.1241 (ttt) cc_final: 0.1026 (ttp) REVERT: E 50 LYS cc_start: 0.7860 (mttt) cc_final: 0.7653 (mtmt) REVERT: E 226 MET cc_start: 0.8796 (mmm) cc_final: 0.8526 (mmm) REVERT: E 292 MET cc_start: 0.8560 (mtm) cc_final: 0.8344 (mtp) REVERT: F 36 MET cc_start: 0.1527 (ttt) cc_final: 0.1243 (ttp) REVERT: F 129 ASP cc_start: 0.6755 (t70) cc_final: 0.6532 (t0) REVERT: F 213 MET cc_start: 0.7766 (ttm) cc_final: 0.7382 (ttp) REVERT: F 363 THR cc_start: 0.7863 (p) cc_final: 0.7572 (m) REVERT: F 732 MET cc_start: 0.7996 (mmp) cc_final: 0.7765 (mmp) outliers start: 6 outliers final: 0 residues processed: 828 average time/residue: 2.9732 time to fit residues: 2939.9526 Evaluate side-chains 662 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 662 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 1.9990 chunk 309 optimal weight: 6.9990 chunk 171 optimal weight: 9.9990 chunk 105 optimal weight: 5.9990 chunk 208 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 238 optimal weight: 10.0000 chunk 370 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 469 GLN A 583 ASN B 91 ASN B 109 HIS B 469 GLN B 583 ASN B 609 ASN C 109 HIS C 202 ASN C 573 ASN C 583 ASN D 109 HIS D 469 GLN D 583 ASN D 655 ASN E 91 ASN E 109 HIS E 469 GLN E 583 ASN E 609 ASN F 109 HIS F 202 ASN F 469 GLN F 573 ASN F 583 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 34926 Z= 0.285 Angle : 0.650 5.298 47022 Z= 0.366 Chirality : 0.045 0.165 4968 Planarity : 0.006 0.061 5904 Dihedral : 4.489 25.932 4572 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.58 % Allowed : 6.23 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.38 (0.13), residues: 4068 helix: 1.27 (0.13), residues: 1404 sheet: 0.77 (0.22), residues: 522 loop : 0.90 (0.14), residues: 2142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 610 HIS 0.010 0.002 HIS A 249 PHE 0.019 0.003 PHE C 156 TYR 0.019 0.003 TYR A 149 ARG 0.010 0.001 ARG B 664 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 692 time to evaluate : 4.302 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: A 36 MET cc_start: 0.1468 (ttt) cc_final: 0.1009 (ttp) REVERT: A 78 ASP cc_start: 0.6016 (p0) cc_final: 0.5696 (p0) REVERT: A 146 MET cc_start: 0.8950 (ttm) cc_final: 0.8711 (ttm) REVERT: A 503 ASP cc_start: 0.6802 (OUTLIER) cc_final: 0.6581 (p0) REVERT: B 451 MET cc_start: 0.8420 (mmm) cc_final: 0.8018 (mmm) REVERT: C 213 MET cc_start: 0.7802 (ttm) cc_final: 0.7428 (ttp) REVERT: C 457 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7307 (ttt90) REVERT: C 479 MET cc_start: 0.8418 (mmm) cc_final: 0.8211 (mmm) REVERT: C 510 MET cc_start: 0.8170 (ttt) cc_final: 0.7764 (ttt) REVERT: D 36 MET cc_start: 0.1469 (ttt) cc_final: 0.1012 (ttp) REVERT: D 146 MET cc_start: 0.8954 (ttm) cc_final: 0.8712 (ttm) REVERT: E 259 ASP cc_start: 0.6594 (p0) cc_final: 0.6392 (p0) REVERT: E 451 MET cc_start: 0.8423 (mmm) cc_final: 0.8020 (mmm) REVERT: F 213 MET cc_start: 0.7799 (ttm) cc_final: 0.7424 (ttp) REVERT: F 457 ARG cc_start: 0.7516 (ttm-80) cc_final: 0.7312 (ttt90) REVERT: F 479 MET cc_start: 0.8431 (mmm) cc_final: 0.8224 (mmm) REVERT: F 510 MET cc_start: 0.8224 (ttt) cc_final: 0.7782 (ttt) REVERT: F 715 MET cc_start: 0.6062 (ptt) cc_final: 0.5603 (ptt) outliers start: 22 outliers final: 8 residues processed: 694 average time/residue: 2.7704 time to fit residues: 2327.0963 Evaluate side-chains 669 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 660 time to evaluate : 4.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain B residue 503 ASP Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain E residue 503 ASP Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain F residue 578 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 308 optimal weight: 8.9990 chunk 252 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 371 optimal weight: 10.0000 chunk 400 optimal weight: 6.9990 chunk 330 optimal weight: 0.9990 chunk 368 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 297 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 469 GLN B 91 ASN B 109 HIS B 609 ASN C 109 HIS C 202 ASN D 109 HIS D 469 GLN D 655 ASN E 91 ASN E 109 HIS E 609 ASN F 109 HIS F 202 ASN F 469 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 34926 Z= 0.320 Angle : 0.707 5.783 47022 Z= 0.398 Chirality : 0.047 0.161 4968 Planarity : 0.006 0.078 5904 Dihedral : 4.851 23.714 4572 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 1.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 0.98 % Allowed : 6.70 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.07 (0.13), residues: 4068 helix: 1.20 (0.13), residues: 1368 sheet: 0.72 (0.23), residues: 480 loop : 0.54 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 591 HIS 0.009 0.002 HIS F 249 PHE 0.019 0.003 PHE F 156 TYR 0.020 0.003 TYR C 149 ARG 0.012 0.002 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 668 time to evaluate : 4.868 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: A 146 MET cc_start: 0.8996 (ttm) cc_final: 0.8776 (ttm) REVERT: A 209 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6930 (mtpt) REVERT: B 226 MET cc_start: 0.8991 (mmm) cc_final: 0.8727 (mmm) REVERT: C 81 MET cc_start: 0.6698 (OUTLIER) cc_final: 0.6299 (mpp) REVERT: C 213 MET cc_start: 0.7821 (ttm) cc_final: 0.7447 (ttp) REVERT: C 457 ARG cc_start: 0.7533 (ttm-80) cc_final: 0.7311 (ttt90) REVERT: C 479 MET cc_start: 0.8409 (mmm) cc_final: 0.8086 (mmm) REVERT: C 510 MET cc_start: 0.8341 (ttt) cc_final: 0.7934 (ttt) REVERT: C 709 MET cc_start: 0.1601 (mmm) cc_final: 0.1284 (tmm) REVERT: D 146 MET cc_start: 0.8998 (ttm) cc_final: 0.8779 (ttm) REVERT: D 209 LYS cc_start: 0.7383 (OUTLIER) cc_final: 0.6932 (mtpt) REVERT: E 226 MET cc_start: 0.8989 (mmm) cc_final: 0.8713 (mmm) REVERT: F 81 MET cc_start: 0.6710 (OUTLIER) cc_final: 0.6305 (mpp) REVERT: F 213 MET cc_start: 0.7817 (ttm) cc_final: 0.7441 (ttp) REVERT: F 457 ARG cc_start: 0.7538 (ttm-80) cc_final: 0.7314 (ttt90) REVERT: F 479 MET cc_start: 0.8418 (mmm) cc_final: 0.8092 (mmm) REVERT: F 510 MET cc_start: 0.8355 (ttt) cc_final: 0.7938 (ttt) REVERT: F 709 MET cc_start: 0.1490 (mmm) cc_final: 0.1156 (tmm) REVERT: F 715 MET cc_start: 0.5843 (ptt) cc_final: 0.5600 (ptm) outliers start: 37 outliers final: 18 residues processed: 680 average time/residue: 2.8434 time to fit residues: 2332.8961 Evaluate side-chains 677 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 655 time to evaluate : 4.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 620 HIS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 620 HIS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain F residue 81 MET Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 620 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 177 optimal weight: 0.9990 chunk 249 optimal weight: 0.9980 chunk 372 optimal weight: 4.9990 chunk 394 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 353 optimal weight: 2.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 469 GLN B 91 ASN B 109 HIS B 181 ASN B 609 ASN C 109 HIS C 202 ASN D 109 HIS D 469 GLN D 655 ASN E 91 ASN E 109 HIS E 181 ASN E 609 ASN F 109 HIS F 202 ASN F 469 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34926 Z= 0.192 Angle : 0.552 5.412 47022 Z= 0.308 Chirality : 0.042 0.143 4968 Planarity : 0.004 0.071 5904 Dihedral : 4.573 21.594 4572 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.87 % Allowed : 7.15 % Favored : 91.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.16 (0.13), residues: 4068 helix: 1.46 (0.13), residues: 1362 sheet: 0.01 (0.21), residues: 570 loop : 0.70 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 591 HIS 0.007 0.001 HIS E 109 PHE 0.014 0.002 PHE E 537 TYR 0.018 0.002 TYR D 149 ARG 0.012 0.001 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 652 time to evaluate : 4.321 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: A 36 MET cc_start: 0.1534 (ttp) cc_final: 0.1311 (ttp) REVERT: A 209 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6899 (mtpt) REVERT: A 593 ARG cc_start: 0.6381 (ptm160) cc_final: 0.6111 (ptm-80) REVERT: B 140 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6927 (mp0) REVERT: B 226 MET cc_start: 0.8923 (mmm) cc_final: 0.8638 (mmm) REVERT: C 213 MET cc_start: 0.7746 (ttm) cc_final: 0.7430 (ttp) REVERT: C 457 ARG cc_start: 0.7526 (ttm-80) cc_final: 0.7212 (ttt90) REVERT: C 479 MET cc_start: 0.8357 (mmm) cc_final: 0.7997 (mmm) REVERT: C 709 MET cc_start: 0.1539 (mmm) cc_final: 0.1221 (tmm) REVERT: D 36 MET cc_start: 0.1528 (ttp) cc_final: 0.1313 (ttp) REVERT: D 209 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6900 (mtpt) REVERT: D 593 ARG cc_start: 0.6370 (ptm160) cc_final: 0.6099 (ptm-80) REVERT: E 140 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6925 (mp0) REVERT: E 226 MET cc_start: 0.8925 (mmm) cc_final: 0.8633 (mmm) REVERT: E 458 GLU cc_start: 0.6686 (mp0) cc_final: 0.6483 (mp0) REVERT: F 36 MET cc_start: 0.0843 (ttp) cc_final: 0.0547 (tmm) REVERT: F 213 MET cc_start: 0.7743 (ttm) cc_final: 0.7426 (ttp) REVERT: F 457 ARG cc_start: 0.7522 (ttm-80) cc_final: 0.7208 (ttt90) REVERT: F 479 MET cc_start: 0.8367 (mmm) cc_final: 0.8006 (mmm) REVERT: F 510 MET cc_start: 0.8303 (ttt) cc_final: 0.7889 (ttt) REVERT: F 709 MET cc_start: 0.1604 (mmm) cc_final: 0.1277 (tmm) outliers start: 33 outliers final: 18 residues processed: 664 average time/residue: 2.8299 time to fit residues: 2265.7416 Evaluate side-chains 665 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 643 time to evaluate : 4.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 620 HIS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 620 HIS Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 578 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 7.9990 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 293 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 336 optimal weight: 9.9990 chunk 272 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 469 GLN B 91 ASN B 109 HIS B 609 ASN C 109 HIS C 202 ASN D 109 HIS D 469 GLN D 609 ASN D 655 ASN E 91 ASN E 109 HIS E 609 ASN F 109 HIS F 202 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34926 Z= 0.272 Angle : 0.647 5.535 47022 Z= 0.363 Chirality : 0.045 0.156 4968 Planarity : 0.006 0.072 5904 Dihedral : 4.764 23.830 4572 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.93 % Allowed : 7.45 % Favored : 91.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.99 (0.13), residues: 4068 helix: 1.25 (0.13), residues: 1362 sheet: 0.10 (0.22), residues: 534 loop : 0.58 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 591 HIS 0.009 0.002 HIS B 109 PHE 0.019 0.003 PHE E 537 TYR 0.021 0.003 TYR A 149 ARG 0.012 0.001 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 649 time to evaluate : 4.361 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: A 36 MET cc_start: 0.1724 (ttp) cc_final: 0.1500 (ttp) REVERT: A 209 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.6925 (mtpt) REVERT: B 140 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6751 (mp0) REVERT: B 706 MET cc_start: 0.2902 (mmt) cc_final: 0.1615 (ptp) REVERT: C 36 MET cc_start: 0.1040 (ttp) cc_final: 0.0778 (tmm) REVERT: C 213 MET cc_start: 0.7805 (ttm) cc_final: 0.7457 (ttp) REVERT: C 457 ARG cc_start: 0.7536 (ttm-80) cc_final: 0.7332 (ttt90) REVERT: C 479 MET cc_start: 0.8410 (mmm) cc_final: 0.8093 (mmm) REVERT: C 709 MET cc_start: 0.1438 (mmm) cc_final: 0.1085 (tmm) REVERT: D 36 MET cc_start: 0.1730 (ttp) cc_final: 0.1500 (ttp) REVERT: D 50 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7653 (mttm) REVERT: D 209 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6925 (mtpt) REVERT: E 140 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: E 706 MET cc_start: 0.2911 (mmt) cc_final: 0.1617 (ptp) REVERT: F 36 MET cc_start: 0.0843 (ttp) cc_final: 0.0590 (tmm) REVERT: F 213 MET cc_start: 0.7799 (ttm) cc_final: 0.7450 (ttp) REVERT: F 457 ARG cc_start: 0.7542 (ttm-80) cc_final: 0.7251 (ttt90) REVERT: F 479 MET cc_start: 0.8420 (mmm) cc_final: 0.8101 (mmm) REVERT: F 510 MET cc_start: 0.8361 (ttt) cc_final: 0.8008 (ttt) REVERT: F 709 MET cc_start: 0.1565 (mmm) cc_final: 0.1198 (tmm) outliers start: 35 outliers final: 26 residues processed: 663 average time/residue: 2.8603 time to fit residues: 2316.7084 Evaluate side-chains 670 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 639 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 501 ARG Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 620 HIS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 620 HIS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 501 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 620 HIS Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 620 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 9.9990 chunk 355 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 394 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 32 optimal weight: 0.4980 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 109 HIS A 469 GLN B 91 ASN B 109 HIS B 609 ASN C 109 HIS C 202 ASN D 109 HIS D 469 GLN D 655 ASN E 91 ASN E 109 HIS E 609 ASN F 109 HIS F 202 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34926 Z= 0.274 Angle : 0.641 5.660 47022 Z= 0.359 Chirality : 0.045 0.154 4968 Planarity : 0.005 0.059 5904 Dihedral : 4.796 23.065 4572 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 1.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.09 % Allowed : 7.53 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.94 (0.13), residues: 4068 helix: 1.23 (0.13), residues: 1362 sheet: 0.05 (0.22), residues: 534 loop : 0.54 (0.14), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 591 HIS 0.009 0.002 HIS D 54 PHE 0.019 0.003 PHE B 537 TYR 0.020 0.003 TYR A 149 ARG 0.010 0.001 ARG C 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 676 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 635 time to evaluate : 4.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 MET cc_start: 0.1766 (ttp) cc_final: 0.1094 (ttp) REVERT: A 209 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.6927 (mtpt) REVERT: B 140 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: B 587 LYS cc_start: 0.7497 (OUTLIER) cc_final: 0.7110 (mmmt) REVERT: B 660 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7441 (mtm110) REVERT: B 715 MET cc_start: 0.7209 (mtm) cc_final: 0.6949 (mtt) REVERT: C 36 MET cc_start: 0.0868 (ttp) cc_final: 0.0665 (tmm) REVERT: C 213 MET cc_start: 0.7796 (ttm) cc_final: 0.7440 (ttp) REVERT: C 457 ARG cc_start: 0.7539 (ttm-80) cc_final: 0.7334 (ttt90) REVERT: C 479 MET cc_start: 0.8405 (mmm) cc_final: 0.8088 (mmm) REVERT: C 709 MET cc_start: 0.1317 (mmm) cc_final: 0.0979 (tmm) REVERT: D 209 LYS cc_start: 0.7381 (OUTLIER) cc_final: 0.6946 (mtpt) REVERT: E 140 GLU cc_start: 0.7285 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: E 587 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.7112 (mmmt) REVERT: E 660 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.7452 (mtm110) REVERT: E 715 MET cc_start: 0.7188 (mtm) cc_final: 0.6932 (mtt) REVERT: F 213 MET cc_start: 0.7781 (ttm) cc_final: 0.7443 (ttp) REVERT: F 457 ARG cc_start: 0.7544 (ttm-80) cc_final: 0.7337 (ttt90) REVERT: F 479 MET cc_start: 0.8416 (mmm) cc_final: 0.8095 (mmm) REVERT: F 510 MET cc_start: 0.8383 (ttt) cc_final: 0.7915 (ttt) REVERT: F 709 MET cc_start: 0.1349 (mmm) cc_final: 0.0976 (tmm) outliers start: 41 outliers final: 26 residues processed: 653 average time/residue: 2.8253 time to fit residues: 2231.6829 Evaluate side-chains 668 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 634 time to evaluate : 4.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 620 HIS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 620 HIS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 587 LYS Chi-restraints excluded: chain E residue 620 HIS Chi-restraints excluded: chain E residue 660 ARG Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 620 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 288 optimal weight: 5.9990 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 2.9990 chunk 393 optimal weight: 7.9990 chunk 246 optimal weight: 7.9990 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 469 GLN B 91 ASN B 109 HIS B 609 ASN C 109 HIS C 202 ASN D 109 HIS D 469 GLN D 655 ASN E 91 ASN E 109 HIS E 609 ASN F 109 HIS F 202 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34926 Z= 0.312 Angle : 0.684 7.202 47022 Z= 0.384 Chirality : 0.046 0.159 4968 Planarity : 0.006 0.057 5904 Dihedral : 4.870 23.820 4572 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.38 % Allowed : 7.21 % Favored : 91.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 0.74 (0.13), residues: 4068 helix: 0.97 (0.13), residues: 1404 sheet: 0.02 (0.22), residues: 534 loop : 0.45 (0.14), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 591 HIS 0.011 0.002 HIS D 54 PHE 0.022 0.003 PHE E 537 TYR 0.022 0.003 TYR A 149 ARG 0.008 0.001 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 645 time to evaluate : 4.326 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: A 209 LYS cc_start: 0.7385 (OUTLIER) cc_final: 0.6937 (mtpt) REVERT: B 140 GLU cc_start: 0.7297 (OUTLIER) cc_final: 0.6788 (mp0) REVERT: B 587 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.7151 (mmtt) REVERT: B 660 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7468 (mtm110) REVERT: B 715 MET cc_start: 0.7181 (mtm) cc_final: 0.6972 (mtt) REVERT: C 129 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6848 (t0) REVERT: C 213 MET cc_start: 0.7810 (ttm) cc_final: 0.7468 (ttp) REVERT: C 479 MET cc_start: 0.8409 (mmm) cc_final: 0.8093 (mmm) REVERT: C 709 MET cc_start: 0.1307 (mmm) cc_final: 0.0966 (tmm) REVERT: D 209 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.6941 (mtpt) REVERT: E 140 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.6783 (mp0) REVERT: E 587 LYS cc_start: 0.7500 (OUTLIER) cc_final: 0.7153 (mmtt) REVERT: E 660 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7444 (mtm110) REVERT: E 715 MET cc_start: 0.7176 (mtm) cc_final: 0.6967 (mtt) REVERT: F 129 ASP cc_start: 0.7075 (OUTLIER) cc_final: 0.6843 (t0) REVERT: F 213 MET cc_start: 0.7807 (ttm) cc_final: 0.7457 (ttp) REVERT: F 479 MET cc_start: 0.8419 (mmm) cc_final: 0.8098 (mmm) REVERT: F 510 MET cc_start: 0.8400 (ttt) cc_final: 0.7924 (ttt) REVERT: F 709 MET cc_start: 0.1319 (mmm) cc_final: 0.0975 (tmm) outliers start: 52 outliers final: 33 residues processed: 667 average time/residue: 2.7467 time to fit residues: 2218.2009 Evaluate side-chains 678 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 635 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 501 ARG Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 129 ASP Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 291 HIS Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 620 HIS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 620 HIS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 501 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 587 LYS Chi-restraints excluded: chain E residue 620 HIS Chi-restraints excluded: chain E residue 660 ARG Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 129 ASP Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 291 HIS Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 620 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 4.9990 chunk 118 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 250 optimal weight: 8.9990 chunk 267 optimal weight: 6.9990 chunk 194 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 309 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 ASN A 109 HIS A 469 GLN B 91 ASN B 109 HIS B 609 ASN C 109 HIS C 202 ASN D 91 ASN D 109 HIS D 469 GLN D 655 ASN E 91 ASN E 109 HIS E 609 ASN F 109 HIS F 202 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 34926 Z= 0.225 Angle : 0.588 5.730 47022 Z= 0.329 Chirality : 0.043 0.148 4968 Planarity : 0.005 0.055 5904 Dihedral : 4.729 22.464 4572 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 1.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.17 % Allowed : 7.55 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 (0.13), residues: 4068 helix: 1.34 (0.13), residues: 1362 sheet: 0.00 (0.21), residues: 546 loop : 0.53 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 591 HIS 0.009 0.002 HIS D 54 PHE 0.018 0.002 PHE B 537 TYR 0.019 0.002 TYR B 337 ARG 0.009 0.001 ARG C 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 647 time to evaluate : 4.290 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: A 209 LYS cc_start: 0.7364 (OUTLIER) cc_final: 0.6909 (mtpt) REVERT: B 140 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: B 587 LYS cc_start: 0.7461 (OUTLIER) cc_final: 0.7136 (mmtt) REVERT: B 660 ARG cc_start: 0.8006 (OUTLIER) cc_final: 0.7439 (mtm110) REVERT: C 213 MET cc_start: 0.7770 (ttm) cc_final: 0.7440 (ttp) REVERT: C 479 MET cc_start: 0.8396 (mmm) cc_final: 0.8052 (mmm) REVERT: C 709 MET cc_start: 0.1308 (mmm) cc_final: 0.0920 (tmm) REVERT: D 209 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.6916 (mtpt) REVERT: E 140 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6991 (mp0) REVERT: E 587 LYS cc_start: 0.7455 (OUTLIER) cc_final: 0.7138 (mmtt) REVERT: E 660 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7431 (mtm110) REVERT: F 213 MET cc_start: 0.7752 (ttm) cc_final: 0.7443 (ttp) REVERT: F 479 MET cc_start: 0.8410 (mmm) cc_final: 0.8091 (mmm) REVERT: F 510 MET cc_start: 0.8375 (ttt) cc_final: 0.7881 (ttt) REVERT: F 709 MET cc_start: 0.1259 (mmm) cc_final: 0.0870 (tmm) outliers start: 44 outliers final: 31 residues processed: 665 average time/residue: 2.8086 time to fit residues: 2250.4371 Evaluate side-chains 681 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 642 time to evaluate : 4.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 140 GLU Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 501 ARG Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 620 HIS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 620 HIS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 501 ARG Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 587 LYS Chi-restraints excluded: chain E residue 620 HIS Chi-restraints excluded: chain E residue 660 ARG Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 620 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 3.9990 chunk 376 optimal weight: 7.9990 chunk 343 optimal weight: 7.9990 chunk 366 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 287 optimal weight: 1.9990 chunk 112 optimal weight: 7.9990 chunk 331 optimal weight: 8.9990 chunk 346 optimal weight: 0.9980 chunk 365 optimal weight: 0.7980 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 109 HIS A 469 GLN B 91 ASN B 109 HIS B 609 ASN C 109 HIS C 202 ASN D 109 HIS D 469 GLN D 655 ASN E 91 ASN E 109 HIS E 609 ASN F 109 HIS F 202 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 34926 Z= 0.192 Angle : 0.555 5.990 47022 Z= 0.308 Chirality : 0.042 0.143 4968 Planarity : 0.004 0.055 5904 Dihedral : 4.611 21.672 4572 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 1.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.01 % Allowed : 7.82 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.11 (0.13), residues: 4068 helix: 1.49 (0.13), residues: 1362 sheet: -0.09 (0.21), residues: 570 loop : 0.64 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 591 HIS 0.008 0.001 HIS A 54 PHE 0.017 0.002 PHE E 537 TYR 0.018 0.002 TYR A 149 ARG 0.009 0.001 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 646 time to evaluate : 4.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6900 (mtpt) REVERT: B 140 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: B 660 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7457 (mtm110) REVERT: B 706 MET cc_start: 0.2744 (mmt) cc_final: 0.1716 (ptp) REVERT: C 213 MET cc_start: 0.7739 (ttm) cc_final: 0.7411 (ttp) REVERT: C 479 MET cc_start: 0.8389 (mmm) cc_final: 0.8047 (mmm) REVERT: C 709 MET cc_start: 0.1310 (mmm) cc_final: 0.0921 (tmm) REVERT: D 209 LYS cc_start: 0.7318 (OUTLIER) cc_final: 0.6887 (mtpt) REVERT: E 140 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6978 (mp0) REVERT: E 660 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7448 (mtm110) REVERT: E 706 MET cc_start: 0.2744 (mmt) cc_final: 0.1711 (ptp) REVERT: F 213 MET cc_start: 0.7724 (ttm) cc_final: 0.7402 (ttp) REVERT: F 479 MET cc_start: 0.8402 (mmm) cc_final: 0.8057 (mmm) REVERT: F 510 MET cc_start: 0.8340 (ttt) cc_final: 0.7885 (ttt) REVERT: F 709 MET cc_start: 0.1313 (mmm) cc_final: 0.0923 (tmm) outliers start: 38 outliers final: 28 residues processed: 664 average time/residue: 2.8112 time to fit residues: 2251.3751 Evaluate side-chains 679 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 645 time to evaluate : 4.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain A residue 715 MET Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 291 HIS Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 620 HIS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 620 HIS Chi-restraints excluded: chain D residue 715 MET Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 620 HIS Chi-restraints excluded: chain E residue 660 ARG Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 578 ASP Chi-restraints excluded: chain F residue 620 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 6.9990 chunk 387 optimal weight: 2.9990 chunk 236 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 269 optimal weight: 0.7980 chunk 406 optimal weight: 7.9990 chunk 374 optimal weight: 0.9990 chunk 323 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 250 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 469 GLN B 91 ASN B 109 HIS B 609 ASN C 109 HIS C 202 ASN D 109 HIS D 469 GLN D 655 ASN E 91 ASN E 109 HIS E 609 ASN F 109 HIS F 202 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34926 Z= 0.181 Angle : 0.542 6.773 47022 Z= 0.300 Chirality : 0.042 0.142 4968 Planarity : 0.004 0.104 5904 Dihedral : 4.559 21.246 4572 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 1.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.01 % Allowed : 8.00 % Favored : 90.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.16 (0.13), residues: 4068 helix: 1.55 (0.13), residues: 1362 sheet: -0.05 (0.21), residues: 570 loop : 0.66 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 591 HIS 0.008 0.001 HIS E 109 PHE 0.016 0.002 PHE B 537 TYR 0.019 0.002 TYR A 491 ARG 0.015 0.001 ARG C 262 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8136 Ramachandran restraints generated. 4068 Oldfield, 0 Emsley, 4068 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 647 time to evaluate : 4.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7338 (OUTLIER) cc_final: 0.6891 (mtpt) REVERT: B 140 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: B 587 LYS cc_start: 0.7422 (OUTLIER) cc_final: 0.7113 (mmtt) REVERT: B 660 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7457 (mtm110) REVERT: B 706 MET cc_start: 0.2652 (mmt) cc_final: 0.1587 (ptp) REVERT: C 213 MET cc_start: 0.7721 (ttm) cc_final: 0.7396 (ttp) REVERT: C 479 MET cc_start: 0.8388 (mmm) cc_final: 0.8047 (mmm) REVERT: C 709 MET cc_start: 0.1301 (mmm) cc_final: 0.0918 (tmm) REVERT: D 41 MET cc_start: 0.5362 (tpp) cc_final: 0.4765 (tpp) REVERT: D 209 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6874 (mtpt) REVERT: E 140 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: E 587 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7117 (mmtt) REVERT: E 660 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7447 (mtm110) REVERT: E 706 MET cc_start: 0.2695 (mmt) cc_final: 0.1608 (ptp) REVERT: F 213 MET cc_start: 0.7708 (ttm) cc_final: 0.7403 (ttp) REVERT: F 479 MET cc_start: 0.8401 (mmm) cc_final: 0.8059 (mmm) REVERT: F 510 MET cc_start: 0.8317 (ttt) cc_final: 0.7873 (ttt) REVERT: F 709 MET cc_start: 0.1306 (mmm) cc_final: 0.0922 (tmm) outliers start: 38 outliers final: 25 residues processed: 664 average time/residue: 2.9164 time to fit residues: 2359.1353 Evaluate side-chains 675 residues out of total 3738 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 642 time to evaluate : 4.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 SER Chi-restraints excluded: chain A residue 209 LYS Chi-restraints excluded: chain A residue 394 SER Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 620 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 394 SER Chi-restraints excluded: chain B residue 578 ASP Chi-restraints excluded: chain B residue 587 LYS Chi-restraints excluded: chain B residue 620 HIS Chi-restraints excluded: chain B residue 660 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 620 HIS Chi-restraints excluded: chain D residue 43 SER Chi-restraints excluded: chain D residue 209 LYS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 578 ASP Chi-restraints excluded: chain D residue 620 HIS Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 291 HIS Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 578 ASP Chi-restraints excluded: chain E residue 587 LYS Chi-restraints excluded: chain E residue 620 HIS Chi-restraints excluded: chain E residue 660 ARG Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 159 SER Chi-restraints excluded: chain F residue 620 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 9.9990 chunk 344 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 298 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 324 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 332 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 HIS A 469 GLN B 91 ASN B 109 HIS B 609 ASN C 109 HIS C 202 ASN D 109 HIS D 469 GLN D 655 ASN E 91 ASN E 109 HIS E 609 ASN F 109 HIS F 202 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.157818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.134266 restraints weight = 88636.195| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 0.73 r_work: 0.3241 rms_B_bonded: 0.92 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 1.74 restraints_weight: 0.2500 r_work: 0.2909 rms_B_bonded: 3.68 restraints_weight: 0.1250 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 34926 Z= 0.174 Angle : 0.535 7.084 47022 Z= 0.295 Chirality : 0.042 0.140 4968 Planarity : 0.004 0.092 5904 Dihedral : 4.509 20.835 4572 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 1.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.98 % Allowed : 8.06 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: 1.22 (0.13), residues: 4068 helix: 1.59 (0.13), residues: 1362 sheet: -0.02 (0.21), residues: 570 loop : 0.69 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 591 HIS 0.009 0.001 HIS B 109 PHE 0.016 0.002 PHE B 537 TYR 0.018 0.002 TYR D 491 ARG 0.012 0.001 ARG F 262 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32297.08 seconds wall clock time: 545 minutes 35.38 seconds (32735.38 seconds total)