Starting phenix.real_space_refine on Tue Apr 16 02:43:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhr_12338/04_2024/7nhr_12338.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhr_12338/04_2024/7nhr_12338.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhr_12338/04_2024/7nhr_12338.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhr_12338/04_2024/7nhr_12338.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhr_12338/04_2024/7nhr_12338.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nhr_12338/04_2024/7nhr_12338.pdb" } resolution = 2.85 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= 0.007 sd= 0.078 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: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 23609 2.51 5 N 6305 2.21 5 O 6984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 58": "OD1" <-> "OD2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A GLU 675": "OE1" <-> "OE2" Residue "A TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B GLU 463": "OE1" <-> "OE2" Residue "B GLU 626": "OE1" <-> "OE2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 675": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 523": "OE1" <-> "OE2" Residue "C TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 669": "OE1" <-> "OE2" Residue "C GLU 675": "OE1" <-> "OE2" Residue "C TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 239": "OD1" <-> "OD2" Residue "D TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 669": "OE1" <-> "OE2" Residue "E GLU 113": "OE1" <-> "OE2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 184": "OE1" <-> "OE2" Residue "E PHE 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 597": "OD1" <-> "OD2" Residue "E TYR 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 715": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 18": "OD1" <-> "OD2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 675": "OE1" <-> "OE2" Residue "F GLU 684": "OE1" <-> "OE2" Residue "G TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 523": "OE1" <-> "OE2" Residue "G GLU 675": "OE1" <-> "OE2" Residue "G TYR 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 18": "OD1" <-> "OD2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 523": "OE1" <-> "OE2" Residue "H TYR 569": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 37011 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "B" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4363 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Chain: "C" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4367 Classifications: {'peptide': 565} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 541} Chain breaks: 3 Chain: "D" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "E" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4050 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 502} Chain breaks: 3 Chain: "F" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "G" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4363 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Chain: "H" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4367 Classifications: {'peptide': 565} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 541} Chain breaks: 3 Time building chain proxies: 18.79, per 1000 atoms: 0.51 Number of scatterers: 37011 At special positions: 0 Unit cell: (159.168, 164.142, 173.261, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 6984 8.00 N 6305 7.00 C 23609 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 14.53 Conformation dependent library (CDL) restraints added in 6.7 seconds 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8878 Finding SS restraints... Secondary structure from input PDB file: 178 helices and 32 sheets defined 52.5% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.94 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.606A pdb=" N GLN A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.877A pdb=" N LYS A 101 " --> pdb=" O MET A 97 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR A 102 " --> pdb=" O ILE A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.611A pdb=" N SER A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 265 removed outlier: 3.821A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN A 259 " --> pdb=" O TYR A 255 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN A 263 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 305 through 336 Processing helix chain 'A' and resid 340 through 366 removed outlier: 3.582A pdb=" N SER A 366 " --> pdb=" O LYS A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 403 removed outlier: 3.646A pdb=" N VAL A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 452 Processing helix chain 'A' and resid 457 through 465 removed outlier: 3.926A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 521 removed outlier: 3.778A pdb=" N PHE A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 591 through 596 removed outlier: 3.686A pdb=" N ILE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE A 596 " --> pdb=" O ALA A 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 591 through 596' Processing helix chain 'A' and resid 615 through 621 Processing helix chain 'A' and resid 622 through 636 removed outlier: 4.058A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASN A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 657 through 659 No H-bonds generated for 'chain 'A' and resid 657 through 659' Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.550A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 708 Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 86 through 94 removed outlier: 3.834A pdb=" N THR B 90 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 219 Processing helix chain 'B' and resid 240 through 278 removed outlier: 3.731A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN B 263 " --> pdb=" O ASN B 259 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 264 " --> pdb=" O ILE B 260 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 Processing helix chain 'B' and resid 425 through 452 Processing helix chain 'B' and resid 457 through 465 removed outlier: 4.068A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.596A pdb=" N PHE B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 554 removed outlier: 3.666A pdb=" N THR B 554 " --> pdb=" O THR B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 591 through 596 removed outlier: 3.593A pdb=" N ILE B 595 " --> pdb=" O ALA B 591 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ILE B 596 " --> pdb=" O ALA B 592 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 591 through 596' Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 622 through 636 removed outlier: 4.081A pdb=" N GLU B 626 " --> pdb=" O HIS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 672 through 686 Processing helix chain 'B' and resid 701 through 708 Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.872A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 240 through 263 removed outlier: 3.661A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 385 through 404 Processing helix chain 'C' and resid 425 through 452 Processing helix chain 'C' and resid 457 through 465 removed outlier: 4.039A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C 465 " --> pdb=" O LEU C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 521 removed outlier: 3.692A pdb=" N PHE C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 554 removed outlier: 3.845A pdb=" N THR C 554 " --> pdb=" O THR C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 575 Processing helix chain 'C' and resid 581 through 588 Processing helix chain 'C' and resid 615 through 620 Processing helix chain 'C' and resid 622 through 636 removed outlier: 4.156A pdb=" N GLU C 626 " --> pdb=" O HIS C 622 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 672 through 686 removed outlier: 3.578A pdb=" N SER C 686 " --> pdb=" O ARG C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 708 removed outlier: 3.545A pdb=" N TYR C 705 " --> pdb=" O LYS C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.587A pdb=" N GLN D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.924A pdb=" N LYS D 101 " --> pdb=" O MET D 97 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 102 " --> pdb=" O ILE D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 removed outlier: 3.712A pdb=" N SER D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 266 removed outlier: 3.712A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS D 246 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN D 263 " --> pdb=" O ASN D 259 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 297 Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 305 through 336 Processing helix chain 'D' and resid 340 through 366 removed outlier: 3.529A pdb=" N SER D 366 " --> pdb=" O LYS D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 404 removed outlier: 3.917A pdb=" N VAL D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 452 Processing helix chain 'D' and resid 457 through 465 removed outlier: 4.087A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 521 removed outlier: 3.511A pdb=" N PHE D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 554 removed outlier: 4.049A pdb=" N THR D 554 " --> pdb=" O THR D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 575 Processing helix chain 'D' and resid 581 through 587 Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.669A pdb=" N ILE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 591 through 595' Processing helix chain 'D' and resid 615 through 620 Processing helix chain 'D' and resid 622 through 636 removed outlier: 4.102A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 672 through 686 removed outlier: 3.616A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 708 removed outlier: 3.671A pdb=" N TYR D 705 " --> pdb=" O LYS D 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.731A pdb=" N THR E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 107 Processing helix chain 'E' and resid 120 through 129 Processing helix chain 'E' and resid 208 through 219 removed outlier: 3.610A pdb=" N SER E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 261 Processing helix chain 'E' and resid 425 through 451 Processing helix chain 'E' and resid 457 through 464 removed outlier: 4.056A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 521 removed outlier: 3.704A pdb=" N PHE E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 553 Processing helix chain 'E' and resid 569 through 575 Processing helix chain 'E' and resid 581 through 587 removed outlier: 3.531A pdb=" N PHE E 585 " --> pdb=" O GLY E 581 " (cutoff:3.500A) Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.616A pdb=" N ILE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 591 through 595' Processing helix chain 'E' and resid 615 through 620 Processing helix chain 'E' and resid 622 through 636 removed outlier: 4.154A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN E 634 " --> pdb=" O ASN E 630 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 657 through 659 No H-bonds generated for 'chain 'E' and resid 657 through 659' Processing helix chain 'E' and resid 672 through 686 Processing helix chain 'E' and resid 701 through 708 Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 86 through 94 removed outlier: 3.529A pdb=" N GLN F 94 " --> pdb=" O THR F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 removed outlier: 3.633A pdb=" N LYS F 101 " --> pdb=" O MET F 97 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR F 102 " --> pdb=" O ILE F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 removed outlier: 3.598A pdb=" N SER F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 266 removed outlier: 3.798A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS F 246 " --> pdb=" O LYS F 242 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN F 263 " --> pdb=" O ASN F 259 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN F 266 " --> pdb=" O ARG F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 297 Proline residue: F 279 - end of helix Processing helix chain 'F' and resid 305 through 336 Processing helix chain 'F' and resid 340 through 366 Processing helix chain 'F' and resid 368 through 403 removed outlier: 4.037A pdb=" N VAL F 374 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER F 403 " --> pdb=" O ASN F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 451 Processing helix chain 'F' and resid 457 through 464 removed outlier: 3.987A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 521 removed outlier: 3.552A pdb=" N PHE F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 554 removed outlier: 3.780A pdb=" N THR F 554 " --> pdb=" O THR F 550 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 574 Processing helix chain 'F' and resid 581 through 587 Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.526A pdb=" N ILE F 595 " --> pdb=" O ALA F 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 591 through 595' Processing helix chain 'F' and resid 615 through 621 removed outlier: 3.551A pdb=" N MET F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 636 removed outlier: 4.151A pdb=" N GLU F 626 " --> pdb=" O HIS F 622 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN F 634 " --> pdb=" O ASN F 630 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 656 Processing helix chain 'F' and resid 672 through 686 removed outlier: 3.530A pdb=" N SER F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 708 Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 86 through 94 removed outlier: 3.847A pdb=" N THR G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 removed outlier: 3.510A pdb=" N SER G 219 " --> pdb=" O ASP G 215 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 277 removed outlier: 3.593A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN G 263 " --> pdb=" O ASN G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 404 Processing helix chain 'G' and resid 425 through 451 Processing helix chain 'G' and resid 457 through 465 removed outlier: 4.027A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY G 465 " --> pdb=" O LEU G 461 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 521 removed outlier: 3.630A pdb=" N PHE G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 554 removed outlier: 3.802A pdb=" N THR G 554 " --> pdb=" O THR G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 569 through 575 Processing helix chain 'G' and resid 581 through 587 Processing helix chain 'G' and resid 591 through 595 removed outlier: 3.922A pdb=" N ILE G 595 " --> pdb=" O ALA G 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 591 through 595' Processing helix chain 'G' and resid 615 through 620 Processing helix chain 'G' and resid 622 through 636 removed outlier: 4.135A pdb=" N GLU G 626 " --> pdb=" O HIS G 622 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLN G 634 " --> pdb=" O ASN G 630 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 672 through 686 removed outlier: 3.517A pdb=" N SER G 686 " --> pdb=" O ARG G 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 701 through 708 Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 86 through 94 removed outlier: 3.904A pdb=" N THR H 90 " --> pdb=" O SER H 86 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 219 Processing helix chain 'H' and resid 240 through 278 removed outlier: 3.551A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLN H 266 " --> pdb=" O ARG H 262 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N ASP H 267 " --> pdb=" O GLN H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 404 Processing helix chain 'H' and resid 425 through 452 Processing helix chain 'H' and resid 457 through 465 removed outlier: 4.037A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY H 465 " --> pdb=" O LEU H 461 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 521 Processing helix chain 'H' and resid 539 through 554 removed outlier: 3.799A pdb=" N THR H 554 " --> pdb=" O THR H 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 569 through 575 Processing helix chain 'H' and resid 581 through 588 Processing helix chain 'H' and resid 591 through 595 removed outlier: 3.829A pdb=" N ILE H 595 " --> pdb=" O ALA H 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 591 through 595' Processing helix chain 'H' and resid 615 through 620 Processing helix chain 'H' and resid 622 through 636 removed outlier: 4.117A pdb=" N GLU H 626 " --> pdb=" O HIS H 622 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 672 through 686 removed outlier: 3.539A pdb=" N SER H 686 " --> pdb=" O ARG H 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 701 through 708 removed outlier: 3.549A pdb=" N TYR H 705 " --> pdb=" O LYS H 701 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 8.573A pdb=" N ILE A 54 " --> pdb=" O ASP A 418 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ASP A 418 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU A 56 " --> pdb=" O VAL A 416 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A 416 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP A 58 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ASN A 414 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU A 60 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.732A pdb=" N ILE A 156 " --> pdb=" O ASN A 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 141 removed outlier: 7.270A pdb=" N ASN A 134 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ILE A 194 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR A 138 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LEU A 190 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU A 140 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N SER A 188 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 473 removed outlier: 7.366A pdb=" N LEU A 695 " --> pdb=" O TYR A 469 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A 471 " --> pdb=" O LEU A 695 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY A 697 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N CYS A 662 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N ILE A 694 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU A 664 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ASN A 696 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ALA A 666 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL A 698 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY A 533 " --> pdb=" O THR A 643 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU A 559 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ASP A 642 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ILE A 561 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 223 removed outlier: 6.924A pdb=" N GLU B 56 " --> pdb=" O PRO B 421 " (cutoff:3.500A) removed outlier: 12.266A pdb=" N ASP B 58 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 12.821A pdb=" N LEU B 60 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 13.287A pdb=" N THR B 417 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 14.610A pdb=" N GLN B 62 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 13.958A pdb=" N ALA B 415 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 141 removed outlier: 7.256A pdb=" N ASN B 134 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE B 194 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 468 through 473 removed outlier: 6.270A pdb=" N CYS B 693 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA B 470 " --> pdb=" O CYS B 693 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N CYS B 662 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ILE B 694 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU B 664 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASN B 696 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ALA B 666 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL B 698 " --> pdb=" O ALA B 666 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY B 533 " --> pdb=" O THR B 643 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 559 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ASP B 642 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE B 561 " --> pdb=" O ASP B 642 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 220 through 224 removed outlier: 6.972A pdb=" N GLU C 56 " --> pdb=" O PRO C 421 " (cutoff:3.500A) removed outlier: 12.104A pdb=" N ASP C 58 " --> pdb=" O PRO C 419 " (cutoff:3.500A) removed outlier: 12.807A pdb=" N LEU C 60 " --> pdb=" O THR C 417 " (cutoff:3.500A) removed outlier: 13.046A pdb=" N THR C 417 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 14.497A pdb=" N GLN C 62 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 13.846A pdb=" N ALA C 415 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 114 removed outlier: 3.737A pdb=" N ILE C 156 " --> pdb=" O ASN C 168 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 134 through 141 removed outlier: 7.322A pdb=" N ASN C 134 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ILE C 194 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU C 190 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU C 140 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N SER C 188 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 468 through 473 removed outlier: 6.271A pdb=" N CYS C 693 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA C 470 " --> pdb=" O CYS C 693 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLY C 692 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY C 533 " --> pdb=" O THR C 643 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 223 removed outlier: 8.448A pdb=" N ILE D 54 " --> pdb=" O ASP D 418 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N ASP D 418 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLU D 56 " --> pdb=" O VAL D 416 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL D 416 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ASP D 58 " --> pdb=" O ASN D 414 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ASN D 414 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N LEU D 60 " --> pdb=" O ILE D 412 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 114 Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 141 removed outlier: 7.280A pdb=" N ASN D 134 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE D 194 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU D 190 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU D 140 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER D 188 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 468 through 473 removed outlier: 7.254A pdb=" N LEU D 695 " --> pdb=" O TYR D 469 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER D 471 " --> pdb=" O LEU D 695 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY D 697 " --> pdb=" O SER D 471 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N CYS D 662 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N ILE D 694 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU D 664 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ASN D 696 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ALA D 666 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL D 698 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY D 533 " --> pdb=" O THR D 643 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU D 559 " --> pdb=" O ILE D 640 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASP D 642 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE D 561 " --> pdb=" O ASP D 642 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 223 removed outlier: 7.096A pdb=" N GLU E 56 " --> pdb=" O PRO E 421 " (cutoff:3.500A) removed outlier: 12.142A pdb=" N ASP E 58 " --> pdb=" O PRO E 419 " (cutoff:3.500A) removed outlier: 12.583A pdb=" N LEU E 60 " --> pdb=" O THR E 417 " (cutoff:3.500A) removed outlier: 12.881A pdb=" N THR E 417 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 14.477A pdb=" N GLN E 62 " --> pdb=" O ALA E 415 " (cutoff:3.500A) removed outlier: 13.888A pdb=" N ALA E 415 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'E' and resid 134 through 141 removed outlier: 7.421A pdb=" N ASN E 134 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE E 194 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU E 190 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LEU E 140 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N SER E 188 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 468 through 473 removed outlier: 6.103A pdb=" N CYS E 693 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA E 470 " --> pdb=" O CYS E 693 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N CYS E 662 " --> pdb=" O GLY E 692 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N ILE E 694 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU E 664 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASN E 696 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ALA E 666 " --> pdb=" O ASN E 696 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N VAL E 698 " --> pdb=" O ALA E 666 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY E 533 " --> pdb=" O THR E 643 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU E 559 " --> pdb=" O ILE E 640 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ASP E 642 " --> pdb=" O LEU E 559 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ILE E 561 " --> pdb=" O ASP E 642 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 223 removed outlier: 6.887A pdb=" N GLU F 56 " --> pdb=" O PRO F 421 " (cutoff:3.500A) removed outlier: 12.243A pdb=" N ASP F 58 " --> pdb=" O PRO F 419 " (cutoff:3.500A) removed outlier: 12.823A pdb=" N LEU F 60 " --> pdb=" O THR F 417 " (cutoff:3.500A) removed outlier: 12.914A pdb=" N THR F 417 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 14.210A pdb=" N GLN F 62 " --> pdb=" O ALA F 415 " (cutoff:3.500A) removed outlier: 13.603A pdb=" N ALA F 415 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 114 removed outlier: 3.574A pdb=" N ILE F 156 " --> pdb=" O ASN F 168 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 134 through 141 removed outlier: 7.434A pdb=" N ASN F 134 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE F 194 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU F 190 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU F 140 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N SER F 188 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 468 through 473 removed outlier: 7.317A pdb=" N LEU F 695 " --> pdb=" O TYR F 469 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER F 471 " --> pdb=" O LEU F 695 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY F 697 " --> pdb=" O SER F 471 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N CYS F 662 " --> pdb=" O GLY F 692 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N ILE F 694 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU F 664 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ASN F 696 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA F 666 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL F 698 " --> pdb=" O ALA F 666 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY F 533 " --> pdb=" O THR F 643 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU F 559 " --> pdb=" O ILE F 640 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASP F 642 " --> pdb=" O LEU F 559 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE F 561 " --> pdb=" O ASP F 642 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 224 removed outlier: 7.001A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'G' and resid 134 through 141 removed outlier: 7.158A pdb=" N ASN G 134 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE G 194 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU G 190 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU G 140 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER G 188 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 468 through 473 removed outlier: 7.324A pdb=" N LEU G 695 " --> pdb=" O TYR G 469 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N SER G 471 " --> pdb=" O LEU G 695 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY G 697 " --> pdb=" O SER G 471 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 220 through 224 removed outlier: 8.593A pdb=" N ILE H 54 " --> pdb=" O ASP H 418 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASP H 418 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 110 through 114 removed outlier: 4.034A pdb=" N ILE H 156 " --> pdb=" O ASN H 168 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 134 through 141 removed outlier: 7.188A pdb=" N ASN H 134 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ILE H 194 " --> pdb=" O ASN H 134 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU H 190 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU H 140 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N SER H 188 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 468 through 473 removed outlier: 6.316A pdb=" N CYS H 693 " --> pdb=" O VAL H 468 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA H 470 " --> pdb=" O CYS H 693 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLY H 533 " --> pdb=" O THR H 643 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU H 559 " --> pdb=" O ILE H 640 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ASP H 642 " --> pdb=" O LEU H 559 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE H 561 " --> pdb=" O ASP H 642 " (cutoff:3.500A) 2105 hydrogen bonds defined for protein. 6201 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: 14.08 Time building geometry restraints manager: 15.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9779 1.33 - 1.45: 5703 1.45 - 1.57: 21873 1.57 - 1.69: 0 1.69 - 1.81: 210 Bond restraints: 37565 Sorted by residual: bond pdb=" N ILE B 63 " pdb=" CA ILE B 63 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.30e-02 5.92e+03 7.27e+00 bond pdb=" N ILE G 260 " pdb=" CA ILE G 260 " ideal model delta sigma weight residual 1.459 1.493 -0.033 1.30e-02 5.92e+03 6.53e+00 bond pdb=" C GLN G 206 " pdb=" N LEU G 207 " ideal model delta sigma weight residual 1.331 1.282 0.049 2.07e-02 2.33e+03 5.63e+00 bond pdb=" N ARG G 262 " pdb=" CA ARG G 262 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.96e+00 bond pdb=" CA LYS D 580 " pdb=" C LYS D 580 " ideal model delta sigma weight residual 1.530 1.505 0.025 1.17e-02 7.31e+03 4.66e+00 ... (remaining 37560 not shown) Histogram of bond angle deviations from ideal: 94.90 - 102.71: 177 102.71 - 110.52: 10346 110.52 - 118.33: 19307 118.33 - 126.15: 20705 126.15 - 133.96: 313 Bond angle restraints: 50848 Sorted by residual: angle pdb=" N GLY B 575 " pdb=" CA GLY B 575 " pdb=" C GLY B 575 " ideal model delta sigma weight residual 112.68 101.32 11.36 1.26e+00 6.30e-01 8.13e+01 angle pdb=" N MET H 573 " pdb=" CA MET H 573 " pdb=" C MET H 573 " ideal model delta sigma weight residual 111.36 119.04 -7.68 1.09e+00 8.42e-01 4.97e+01 angle pdb=" N THR A 229 " pdb=" CA THR A 229 " pdb=" C THR A 229 " ideal model delta sigma weight residual 110.35 119.45 -9.10 1.36e+00 5.41e-01 4.48e+01 angle pdb=" N LYS H 580 " pdb=" CA LYS H 580 " pdb=" C LYS H 580 " ideal model delta sigma weight residual 111.52 120.07 -8.55 1.40e+00 5.10e-01 3.73e+01 angle pdb=" N GLY A 603 " pdb=" CA GLY A 603 " pdb=" C GLY A 603 " ideal model delta sigma weight residual 114.64 106.91 7.73 1.40e+00 5.10e-01 3.05e+01 ... (remaining 50843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 21540 17.94 - 35.88: 1262 35.88 - 53.82: 141 53.82 - 71.76: 35 71.76 - 89.70: 20 Dihedral angle restraints: 22998 sinusoidal: 9220 harmonic: 13778 Sorted by residual: dihedral pdb=" CA HIS F 576 " pdb=" C HIS F 576 " pdb=" N LYS F 577 " pdb=" CA LYS F 577 " ideal model delta harmonic sigma weight residual 180.00 150.05 29.95 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA HIS D 576 " pdb=" C HIS D 576 " pdb=" N LYS D 577 " pdb=" CA LYS D 577 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA HIS G 576 " pdb=" C HIS G 576 " pdb=" N LYS G 577 " pdb=" CA LYS G 577 " ideal model delta harmonic sigma weight residual 180.00 151.54 28.46 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 22995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5323 0.075 - 0.149: 686 0.149 - 0.224: 10 0.224 - 0.298: 5 0.298 - 0.373: 4 Chirality restraints: 6028 Sorted by residual: chirality pdb=" CA LYS H 580 " pdb=" N LYS H 580 " pdb=" C LYS H 580 " pdb=" CB LYS H 580 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA LYS D 580 " pdb=" N LYS D 580 " pdb=" C LYS D 580 " pdb=" CB LYS D 580 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" CA LYS B 580 " pdb=" N LYS B 580 " pdb=" C LYS B 580 " pdb=" CB LYS B 580 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.75e+00 ... (remaining 6025 not shown) Planarity restraints: 6509 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS H 622 " 0.048 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO H 623 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO H 623 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO H 623 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 131 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO E 132 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 132 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 132 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 197 " -0.033 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO B 198 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO B 198 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 198 " -0.028 5.00e-02 4.00e+02 ... (remaining 6506 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 143 2.42 - 3.04: 23588 3.04 - 3.66: 55979 3.66 - 4.28: 86156 4.28 - 4.90: 142573 Nonbonded interactions: 308439 Sorted by model distance: nonbonded pdb=" OG SER D 86 " pdb=" OD2 ASP D 224 " model vdw 1.796 2.440 nonbonded pdb=" O ASP F 224 " pdb=" O MET F 231 " model vdw 1.924 3.040 nonbonded pdb=" O ASP B 224 " pdb=" O MET B 231 " model vdw 2.036 3.040 nonbonded pdb=" OE1 GLU H 89 " pdb=" OH TYR H 255 " model vdw 2.041 2.440 nonbonded pdb=" OE1 GLU B 89 " pdb=" OH TYR B 255 " model vdw 2.100 2.440 ... (remaining 308434 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 279 or resid 385 through 721)) selection = chain 'B' selection = (chain 'C' and (resid 17 through 279 or resid 385 through 721)) selection = (chain 'D' and (resid 17 through 279 or resid 385 through 721)) selection = (chain 'F' and (resid 17 through 279 or resid 385 through 721)) selection = chain 'G' selection = (chain 'H' and (resid 17 through 279 or resid 385 through 721)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 12.690 Check model and map are aligned: 0.550 Set scattering table: 0.350 Process input model: 93.890 Find NCS groups from input model: 2.990 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 37565 Z= 0.361 Angle : 0.700 11.520 50848 Z= 0.393 Chirality : 0.048 0.373 6028 Planarity : 0.004 0.073 6509 Dihedral : 11.665 89.700 14120 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.02 % Allowed : 0.34 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: -0.14 (0.12), residues: 4708 helix: 0.90 (0.11), residues: 2348 sheet: -0.03 (0.18), residues: 719 loop : -1.56 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 631 HIS 0.006 0.001 HIS H 710 PHE 0.030 0.002 PHE H 574 TYR 0.022 0.002 TYR B 606 ARG 0.020 0.001 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 627 time to evaluate : 4.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LEU cc_start: 0.8295 (mp) cc_final: 0.7817 (mp) REVERT: A 193 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7401 (tm-30) REVERT: D 185 LYS cc_start: 0.7798 (mppt) cc_final: 0.7408 (tptp) REVERT: D 187 ILE cc_start: 0.8599 (mt) cc_final: 0.8370 (mp) REVERT: D 394 ARG cc_start: 0.7874 (ttm-80) cc_final: 0.7464 (ttm-80) REVERT: D 621 MET cc_start: 0.8811 (mtp) cc_final: 0.8586 (mtm) REVERT: E 136 ASP cc_start: 0.8143 (t70) cc_final: 0.7749 (t0) REVERT: G 139 ARG cc_start: 0.7564 (ttt-90) cc_final: 0.7264 (ttt90) REVERT: G 174 LEU cc_start: 0.8331 (mp) cc_final: 0.7362 (mp) REVERT: H 101 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7957 (tttm) REVERT: H 177 VAL cc_start: 0.9189 (t) cc_final: 0.8967 (t) outliers start: 1 outliers final: 4 residues processed: 628 average time/residue: 1.3211 time to fit residues: 1024.1364 Evaluate side-chains 468 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 464 time to evaluate : 4.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 136 ASP Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain H residue 228 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 400 optimal weight: 0.6980 chunk 359 optimal weight: 1.9990 chunk 199 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 242 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 chunk 371 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 225 optimal weight: 0.0770 chunk 276 optimal weight: 0.8980 chunk 430 optimal weight: 9.9990 overall best weight: 0.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 ASN A 361 ASN A 393 ASN A 589 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN B 263 GLN B 571 HIS D 320 ASN D 323 ASN D 390 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 408 ASN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 ASN G 114 GLN G 175 ASN G 206 GLN G 611 GLN H 175 ASN H 420 ASN H 710 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 37565 Z= 0.207 Angle : 0.599 11.660 50848 Z= 0.301 Chirality : 0.044 0.352 6028 Planarity : 0.004 0.060 6509 Dihedral : 4.747 86.529 5118 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.01 % Allowed : 9.06 % Favored : 88.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.51 (0.12), residues: 4708 helix: 1.52 (0.11), residues: 2380 sheet: 0.28 (0.18), residues: 713 loop : -1.46 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 631 HIS 0.005 0.001 HIS G 712 PHE 0.022 0.001 PHE D 273 TYR 0.017 0.001 TYR D 388 ARG 0.007 0.000 ARG D 21 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 543 time to evaluate : 4.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.7758 (tm-30) cc_final: 0.7101 (tm-30) REVERT: A 321 GLN cc_start: 0.9146 (mt0) cc_final: 0.8863 (mp10) REVERT: A 323 ASN cc_start: 0.8442 (t0) cc_final: 0.8176 (t0) REVERT: A 398 LEU cc_start: 0.8881 (tt) cc_final: 0.8657 (mm) REVERT: B 193 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7710 (tm-30) REVERT: B 707 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7130 (tpt-90) REVERT: C 228 ASP cc_start: 0.6977 (m-30) cc_final: 0.6747 (m-30) REVERT: C 446 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7990 (tp) REVERT: C 621 MET cc_start: 0.8544 (mtp) cc_final: 0.8297 (mtp) REVERT: D 390 GLN cc_start: 0.7598 (tm130) cc_final: 0.6996 (tm-30) REVERT: E 136 ASP cc_start: 0.8187 (t70) cc_final: 0.7789 (p0) REVERT: E 408 ASN cc_start: 0.4906 (t0) cc_final: 0.4412 (t0) REVERT: E 680 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.8252 (mtt) REVERT: F 103 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8591 (mp) REVERT: F 195 ASP cc_start: 0.8213 (t0) cc_final: 0.7730 (t0) REVERT: G 23 ILE cc_start: 0.8897 (mm) cc_final: 0.8643 (mp) REVERT: G 139 ARG cc_start: 0.7582 (ttt-90) cc_final: 0.7359 (ttp80) REVERT: G 181 LEU cc_start: 0.8504 (tt) cc_final: 0.8295 (tt) REVERT: G 414 ASN cc_start: 0.8020 (p0) cc_final: 0.7721 (p0) REVERT: H 89 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7164 (mm-30) REVERT: H 103 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8940 (mp) REVERT: H 184 GLU cc_start: 0.8121 (mp0) cc_final: 0.7861 (mp0) outliers start: 82 outliers final: 25 residues processed: 575 average time/residue: 1.2758 time to fit residues: 913.6405 Evaluate side-chains 500 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 470 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain C residue 156 ILE Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 505 LEU Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 522 MET Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 136 ASP Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 408 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 239 optimal weight: 4.9990 chunk 133 optimal weight: 0.7980 chunk 358 optimal weight: 0.6980 chunk 293 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 431 optimal weight: 4.9990 chunk 465 optimal weight: 3.9990 chunk 384 optimal weight: 7.9990 chunk 427 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 345 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 393 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN H 420 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37565 Z= 0.179 Angle : 0.572 12.726 50848 Z= 0.285 Chirality : 0.043 0.177 6028 Planarity : 0.003 0.054 6509 Dihedral : 4.313 60.494 5112 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.50 % Allowed : 10.97 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.86 (0.12), residues: 4708 helix: 1.82 (0.11), residues: 2396 sheet: 0.45 (0.18), residues: 711 loop : -1.34 (0.14), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 631 HIS 0.003 0.000 HIS D 710 PHE 0.024 0.001 PHE D 273 TYR 0.017 0.001 TYR D 388 ARG 0.009 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 514 time to evaluate : 4.193 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: A 193 GLU cc_start: 0.7676 (tm-30) cc_final: 0.6940 (tm-30) REVERT: A 210 LEU cc_start: 0.8441 (mm) cc_final: 0.7824 (tp) REVERT: A 323 ASN cc_start: 0.8340 (t0) cc_final: 0.7960 (t0) REVERT: A 394 ARG cc_start: 0.8468 (mtp85) cc_final: 0.7738 (ttp-170) REVERT: B 136 ASP cc_start: 0.7638 (t70) cc_final: 0.7340 (t0) REVERT: B 193 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7570 (tm-30) REVERT: B 262 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7350 (mtm-85) REVERT: B 707 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7076 (tpt-90) REVERT: C 52 THR cc_start: 0.8858 (p) cc_final: 0.8648 (t) REVERT: C 228 ASP cc_start: 0.6929 (m-30) cc_final: 0.6719 (m-30) REVERT: C 410 ARG cc_start: 0.7777 (mtm-85) cc_final: 0.7471 (mtp85) REVERT: C 452 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7230 (ptt-90) REVERT: C 456 GLU cc_start: 0.7360 (OUTLIER) cc_final: 0.7101 (mt-10) REVERT: C 573 MET cc_start: 0.7932 (ttm) cc_final: 0.7585 (ptp) REVERT: C 621 MET cc_start: 0.8483 (mtp) cc_final: 0.8227 (mtp) REVERT: D 195 ASP cc_start: 0.8360 (t70) cc_final: 0.8099 (t0) REVERT: D 320 ASN cc_start: 0.8393 (m-40) cc_final: 0.8123 (m110) REVERT: E 136 ASP cc_start: 0.8110 (t70) cc_final: 0.7863 (p0) REVERT: E 408 ASN cc_start: 0.4808 (t0) cc_final: 0.4246 (t0) REVERT: E 522 MET cc_start: 0.7732 (mtm) cc_final: 0.7477 (mtt) REVERT: E 680 MET cc_start: 0.8595 (mtm) cc_final: 0.8324 (mtt) REVERT: E 707 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7875 (ttt180) REVERT: F 103 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8509 (mp) REVERT: F 195 ASP cc_start: 0.8362 (t0) cc_final: 0.7921 (t0) REVERT: G 23 ILE cc_start: 0.8893 (mm) cc_final: 0.8642 (mp) REVERT: G 139 ARG cc_start: 0.7549 (ttt-90) cc_final: 0.7305 (ttp80) REVERT: G 174 LEU cc_start: 0.8343 (tm) cc_final: 0.7946 (mp) REVERT: G 181 LEU cc_start: 0.8560 (tt) cc_final: 0.8334 (tt) REVERT: G 414 ASN cc_start: 0.7935 (p0) cc_final: 0.7697 (p0) REVERT: H 103 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8863 (mp) REVERT: H 447 PHE cc_start: 0.7938 (OUTLIER) cc_final: 0.7721 (m-10) outliers start: 102 outliers final: 31 residues processed: 556 average time/residue: 1.2906 time to fit residues: 895.6290 Evaluate side-chains 511 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 472 time to evaluate : 4.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 175 ASN Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 408 ASN Chi-restraints excluded: chain H residue 447 PHE Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 426 optimal weight: 0.6980 chunk 324 optimal weight: 9.9990 chunk 223 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 205 optimal weight: 9.9990 chunk 289 optimal weight: 0.8980 chunk 432 optimal weight: 9.9990 chunk 458 optimal weight: 4.9990 chunk 226 optimal weight: 2.9990 chunk 410 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 371 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 GLN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 671 ASN H 175 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 37565 Z= 0.230 Angle : 0.590 11.872 50848 Z= 0.292 Chirality : 0.044 0.286 6028 Planarity : 0.003 0.052 6509 Dihedral : 4.299 57.495 5112 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.53 % Allowed : 12.15 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.12), residues: 4708 helix: 1.91 (0.11), residues: 2396 sheet: 0.50 (0.18), residues: 715 loop : -1.26 (0.14), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 631 HIS 0.003 0.001 HIS D 710 PHE 0.024 0.001 PHE D 273 TYR 0.015 0.001 TYR G 569 ARG 0.010 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 513 time to evaluate : 4.383 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 193 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6894 (tm-30) REVERT: A 210 LEU cc_start: 0.8423 (mm) cc_final: 0.7835 (tp) REVERT: A 323 ASN cc_start: 0.8329 (t0) cc_final: 0.7901 (t0) REVERT: A 394 ARG cc_start: 0.8367 (mtp85) cc_final: 0.7718 (ttp-110) REVERT: B 136 ASP cc_start: 0.7686 (t70) cc_final: 0.7354 (t0) REVERT: B 137 ILE cc_start: 0.8733 (mt) cc_final: 0.8470 (mm) REVERT: B 156 ILE cc_start: 0.8282 (mt) cc_final: 0.8045 (mp) REVERT: B 193 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7427 (tm-30) REVERT: B 242 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7533 (mtmm) REVERT: B 707 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.7079 (tpt-90) REVERT: C 52 THR cc_start: 0.8839 (p) cc_final: 0.8623 (t) REVERT: C 446 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8038 (tp) REVERT: C 452 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7231 (ptt-90) REVERT: C 456 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.7116 (mt-10) REVERT: E 136 ASP cc_start: 0.8062 (t70) cc_final: 0.7846 (p0) REVERT: E 139 ARG cc_start: 0.8122 (tpt170) cc_final: 0.7870 (ttp80) REVERT: E 408 ASN cc_start: 0.4857 (t0) cc_final: 0.4339 (t0) REVERT: E 680 MET cc_start: 0.8616 (mtm) cc_final: 0.8368 (mtt) REVERT: E 707 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7873 (ttt-90) REVERT: F 103 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8542 (mp) REVERT: F 195 ASP cc_start: 0.8412 (t0) cc_final: 0.8061 (t0) REVERT: F 410 ARG cc_start: 0.7822 (ptm160) cc_final: 0.7085 (ptt180) REVERT: F 651 ASP cc_start: 0.8900 (OUTLIER) cc_final: 0.8520 (m-30) REVERT: G 23 ILE cc_start: 0.8898 (mm) cc_final: 0.8641 (mp) REVERT: G 139 ARG cc_start: 0.7522 (ttt-90) cc_final: 0.7260 (ttp80) REVERT: G 181 LEU cc_start: 0.8581 (tt) cc_final: 0.8311 (tt) REVERT: H 103 ILE cc_start: 0.9138 (OUTLIER) cc_final: 0.8930 (mp) outliers start: 103 outliers final: 41 residues processed: 562 average time/residue: 1.2941 time to fit residues: 908.1616 Evaluate side-chains 522 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 472 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 168 ASN Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 651 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 167 ILE Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 408 ASN Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 540 MET Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 381 optimal weight: 1.9990 chunk 260 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 341 optimal weight: 0.5980 chunk 189 optimal weight: 0.7980 chunk 390 optimal weight: 0.0670 chunk 316 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 233 optimal weight: 0.9980 chunk 411 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 293 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 320 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 671 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37565 Z= 0.165 Angle : 0.567 12.761 50848 Z= 0.280 Chirality : 0.043 0.318 6028 Planarity : 0.003 0.052 6509 Dihedral : 4.115 54.145 5112 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.28 % Allowed : 13.89 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.12), residues: 4708 helix: 2.10 (0.11), residues: 2392 sheet: 0.61 (0.18), residues: 707 loop : -1.24 (0.14), residues: 1609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 631 HIS 0.006 0.000 HIS G 712 PHE 0.025 0.001 PHE D 273 TYR 0.012 0.001 TYR H 255 ARG 0.010 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 503 time to evaluate : 4.112 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: A 193 GLU cc_start: 0.7704 (tm-30) cc_final: 0.6848 (tm-30) REVERT: A 210 LEU cc_start: 0.8355 (mm) cc_final: 0.7773 (tp) REVERT: A 323 ASN cc_start: 0.8333 (t0) cc_final: 0.7944 (t0) REVERT: A 376 ARG cc_start: 0.7505 (ttp80) cc_final: 0.7076 (ttp80) REVERT: A 394 ARG cc_start: 0.8371 (mtp85) cc_final: 0.7770 (ttp-170) REVERT: B 136 ASP cc_start: 0.7627 (t70) cc_final: 0.7275 (t0) REVERT: B 137 ILE cc_start: 0.8698 (mt) cc_final: 0.8328 (mp) REVERT: B 156 ILE cc_start: 0.8285 (mt) cc_final: 0.8065 (mp) REVERT: B 174 LEU cc_start: 0.8423 (mm) cc_final: 0.8195 (mp) REVERT: B 193 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7356 (tm-30) REVERT: C 410 ARG cc_start: 0.7695 (mtm-85) cc_final: 0.7403 (mtp85) REVERT: C 452 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.7219 (ptt-90) REVERT: C 456 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.7037 (mt-10) REVERT: C 573 MET cc_start: 0.7939 (ttm) cc_final: 0.7559 (ptp) REVERT: D 144 ASP cc_start: 0.8356 (t0) cc_final: 0.8112 (t0) REVERT: D 256 LEU cc_start: 0.8241 (tp) cc_final: 0.7918 (tp) REVERT: D 388 TYR cc_start: 0.8819 (t80) cc_final: 0.8596 (t80) REVERT: E 408 ASN cc_start: 0.4932 (t0) cc_final: 0.4416 (t0) REVERT: E 680 MET cc_start: 0.8585 (mtm) cc_final: 0.8365 (mtt) REVERT: E 707 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7868 (ttt180) REVERT: F 103 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8517 (mp) REVERT: F 210 LEU cc_start: 0.8117 (mm) cc_final: 0.7577 (tp) REVERT: F 367 MET cc_start: 0.7629 (tmm) cc_final: 0.6662 (pmm) REVERT: F 522 MET cc_start: 0.7244 (ptp) cc_final: 0.6845 (ptm) REVERT: F 680 MET cc_start: 0.8363 (mtm) cc_final: 0.8145 (mmm) REVERT: G 23 ILE cc_start: 0.8886 (mm) cc_final: 0.8641 (mp) REVERT: G 139 ARG cc_start: 0.7541 (ttt-90) cc_final: 0.7291 (ttp80) REVERT: G 181 LEU cc_start: 0.8534 (tt) cc_final: 0.8271 (tt) REVERT: G 414 ASN cc_start: 0.7806 (p0) cc_final: 0.7583 (p0) REVERT: G 681 LYS cc_start: 0.8673 (mttt) cc_final: 0.8427 (mtmp) REVERT: H 63 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7335 (pp) REVERT: H 103 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8860 (mp) outliers start: 93 outliers final: 43 residues processed: 549 average time/residue: 0.9679 time to fit residues: 665.9888 Evaluate side-chains 523 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 474 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 324 GLU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 63 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 408 ASN Chi-restraints excluded: chain H residue 606 TYR Chi-restraints excluded: chain H residue 704 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 154 optimal weight: 3.9990 chunk 412 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 269 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 458 optimal weight: 4.9990 chunk 380 optimal weight: 0.0870 chunk 212 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN D 323 ASN ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 GLN ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 ASN ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN H 671 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 37565 Z= 0.335 Angle : 0.642 11.706 50848 Z= 0.319 Chirality : 0.046 0.301 6028 Planarity : 0.004 0.053 6509 Dihedral : 4.423 53.525 5112 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.99 % Allowed : 13.77 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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 (0.12), residues: 4708 helix: 1.91 (0.11), residues: 2369 sheet: 0.59 (0.19), residues: 686 loop : -1.20 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 631 HIS 0.004 0.001 HIS D 571 PHE 0.022 0.002 PHE D 273 TYR 0.018 0.002 TYR E 165 ARG 0.007 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 493 time to evaluate : 4.681 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 193 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6811 (tm-30) REVERT: A 210 LEU cc_start: 0.8424 (mm) cc_final: 0.7833 (tp) REVERT: A 323 ASN cc_start: 0.8395 (t0) cc_final: 0.7861 (t0) REVERT: A 388 TYR cc_start: 0.8661 (t80) cc_final: 0.8357 (t80) REVERT: A 394 ARG cc_start: 0.8378 (mtp85) cc_final: 0.7745 (ttp-170) REVERT: B 136 ASP cc_start: 0.7668 (t70) cc_final: 0.7363 (t0) REVERT: B 137 ILE cc_start: 0.8701 (mt) cc_final: 0.8432 (mm) REVERT: B 168 ASN cc_start: 0.7053 (OUTLIER) cc_final: 0.6777 (t0) REVERT: B 193 GLU cc_start: 0.7585 (tm-30) cc_final: 0.7347 (tm-30) REVERT: B 242 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7583 (mtmm) REVERT: C 452 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7128 (ptt-90) REVERT: D 225 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7541 (pt) REVERT: E 139 ARG cc_start: 0.8050 (tpt170) cc_final: 0.7829 (ttp80) REVERT: E 408 ASN cc_start: 0.5033 (t0) cc_final: 0.4693 (t0) REVERT: E 680 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8398 (mtt) REVERT: F 103 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8663 (mp) REVERT: F 195 ASP cc_start: 0.8440 (t0) cc_final: 0.8146 (t0) REVERT: F 210 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7639 (tp) REVERT: F 367 MET cc_start: 0.7554 (tmm) cc_final: 0.6795 (pmm) REVERT: F 525 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7997 (ptpt) REVERT: F 651 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8494 (m-30) REVERT: G 23 ILE cc_start: 0.8898 (mm) cc_final: 0.8651 (mp) REVERT: G 139 ARG cc_start: 0.7553 (ttt-90) cc_final: 0.7241 (ttp80) REVERT: G 181 LEU cc_start: 0.8546 (tt) cc_final: 0.8275 (tt) REVERT: G 414 ASN cc_start: 0.7978 (p0) cc_final: 0.7717 (p0) REVERT: H 89 GLU cc_start: 0.7319 (mm-30) cc_final: 0.7063 (mm-30) REVERT: H 425 LYS cc_start: 0.7690 (mttt) cc_final: 0.7470 (mttp) outliers start: 122 outliers final: 55 residues processed: 560 average time/residue: 1.0935 time to fit residues: 769.1883 Evaluate side-chains 529 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 465 time to evaluate : 3.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 168 ASN Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 242 LYS Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 258 GLN Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 708 TYR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 525 LYS Chi-restraints excluded: chain F residue 651 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 235 THR Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 408 ASN Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Chi-restraints excluded: chain H residue 704 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 442 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 261 optimal weight: 0.0970 chunk 334 optimal weight: 0.5980 chunk 259 optimal weight: 0.6980 chunk 386 optimal weight: 20.0000 chunk 256 optimal weight: 0.6980 chunk 456 optimal weight: 1.9990 chunk 285 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 317 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 671 ASN ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 671 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 37565 Z= 0.171 Angle : 0.593 14.398 50848 Z= 0.292 Chirality : 0.044 0.348 6028 Planarity : 0.003 0.060 6509 Dihedral : 4.127 51.397 5112 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.01 % Allowed : 15.29 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.18 (0.12), residues: 4708 helix: 2.07 (0.11), residues: 2398 sheet: 0.67 (0.19), residues: 685 loop : -1.18 (0.14), residues: 1625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 631 HIS 0.003 0.000 HIS D 710 PHE 0.022 0.001 PHE D 273 TYR 0.021 0.001 TYR D 388 ARG 0.011 0.000 ARG D 379 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 494 time to evaluate : 4.564 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: A 19 LEU cc_start: 0.8714 (tt) cc_final: 0.8323 (tp) REVERT: A 23 ILE cc_start: 0.9255 (OUTLIER) cc_final: 0.9013 (mp) REVERT: A 193 GLU cc_start: 0.7650 (tm-30) cc_final: 0.6764 (tm-30) REVERT: A 210 LEU cc_start: 0.8334 (mm) cc_final: 0.7778 (tp) REVERT: A 262 ARG cc_start: 0.6153 (tmm-80) cc_final: 0.5855 (tmm-80) REVERT: A 323 ASN cc_start: 0.8356 (t0) cc_final: 0.7805 (t0) REVERT: A 372 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7580 (pm20) REVERT: A 388 TYR cc_start: 0.8492 (t80) cc_final: 0.8255 (t80) REVERT: A 394 ARG cc_start: 0.8358 (mtp85) cc_final: 0.7777 (ttp-170) REVERT: B 136 ASP cc_start: 0.7564 (t70) cc_final: 0.7278 (t0) REVERT: B 137 ILE cc_start: 0.8626 (mt) cc_final: 0.8273 (mp) REVERT: B 193 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7278 (tm-30) REVERT: B 195 ASP cc_start: 0.8736 (t70) cc_final: 0.8329 (t0) REVERT: C 410 ARG cc_start: 0.7708 (mtm-85) cc_final: 0.7381 (mtp85) REVERT: C 452 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7158 (ptt-90) REVERT: C 456 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: D 144 ASP cc_start: 0.8336 (t0) cc_final: 0.8099 (t0) REVERT: D 225 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7424 (pt) REVERT: E 408 ASN cc_start: 0.4843 (t0) cc_final: 0.4474 (t0) REVERT: E 680 MET cc_start: 0.8586 (mtm) cc_final: 0.8364 (mtt) REVERT: E 707 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7866 (ttt180) REVERT: F 103 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8495 (mp) REVERT: F 210 LEU cc_start: 0.8169 (mm) cc_final: 0.7620 (tp) REVERT: F 367 MET cc_start: 0.7316 (tmm) cc_final: 0.6855 (pmm) REVERT: F 651 ASP cc_start: 0.8898 (OUTLIER) cc_final: 0.8437 (m-30) REVERT: F 680 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.8141 (mmm) REVERT: G 23 ILE cc_start: 0.8869 (mm) cc_final: 0.8629 (mp) REVERT: G 139 ARG cc_start: 0.7500 (ttt-90) cc_final: 0.7229 (ttp80) REVERT: G 181 LEU cc_start: 0.8561 (tt) cc_final: 0.8313 (tt) REVERT: G 414 ASN cc_start: 0.7844 (p0) cc_final: 0.7620 (p0) REVERT: G 681 LYS cc_start: 0.8692 (mttt) cc_final: 0.8419 (mtmp) outliers start: 82 outliers final: 43 residues processed: 542 average time/residue: 1.3249 time to fit residues: 910.1755 Evaluate side-chains 512 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 460 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 372 GLN Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 651 ASP Chi-restraints excluded: chain F residue 680 MET Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 541 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 408 ASN Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Chi-restraints excluded: chain H residue 704 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 5.9990 chunk 182 optimal weight: 5.9990 chunk 272 optimal weight: 0.9980 chunk 137 optimal weight: 3.9990 chunk 89 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 290 optimal weight: 3.9990 chunk 311 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 359 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 GLN ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 37565 Z= 0.312 Angle : 0.655 14.063 50848 Z= 0.323 Chirality : 0.046 0.335 6028 Planarity : 0.004 0.052 6509 Dihedral : 4.348 50.982 5112 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.53 % Allowed : 15.61 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 1.05 (0.12), residues: 4708 helix: 1.92 (0.11), residues: 2369 sheet: 0.66 (0.19), residues: 706 loop : -1.15 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 631 HIS 0.003 0.001 HIS D 571 PHE 0.046 0.002 PHE D 273 TYR 0.014 0.001 TYR D 141 ARG 0.018 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 479 time to evaluate : 4.308 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 193 GLU cc_start: 0.7641 (tm-30) cc_final: 0.6745 (tm-30) REVERT: A 210 LEU cc_start: 0.8404 (mm) cc_final: 0.7806 (tp) REVERT: A 323 ASN cc_start: 0.8416 (t0) cc_final: 0.7946 (t0) REVERT: A 398 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8625 (pp) REVERT: A 444 LEU cc_start: 0.8625 (mp) cc_final: 0.8424 (mt) REVERT: B 124 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7984 (pp) REVERT: B 136 ASP cc_start: 0.7536 (t70) cc_final: 0.7272 (t0) REVERT: B 137 ILE cc_start: 0.8628 (mt) cc_final: 0.8237 (mp) REVERT: B 184 GLU cc_start: 0.7491 (mp0) cc_final: 0.7263 (mp0) REVERT: B 193 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7277 (tm-30) REVERT: B 195 ASP cc_start: 0.8776 (t70) cc_final: 0.8373 (t0) REVERT: B 262 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7208 (mtm-85) REVERT: C 452 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7138 (ptt-90) REVERT: D 63 ILE cc_start: 0.7913 (OUTLIER) cc_final: 0.7665 (mm) REVERT: D 144 ASP cc_start: 0.8348 (t0) cc_final: 0.8115 (t0) REVERT: D 225 LEU cc_start: 0.7788 (OUTLIER) cc_final: 0.7469 (pt) REVERT: E 139 ARG cc_start: 0.7967 (tpt170) cc_final: 0.7469 (ttp80) REVERT: E 408 ASN cc_start: 0.5080 (t0) cc_final: 0.4787 (t0) REVERT: E 680 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8390 (mtt) REVERT: F 103 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8644 (mp) REVERT: F 195 ASP cc_start: 0.8440 (t0) cc_final: 0.8141 (OUTLIER) REVERT: F 210 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7632 (tp) REVERT: F 367 MET cc_start: 0.7297 (tmm) cc_final: 0.7056 (pmt) REVERT: F 651 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8453 (m-30) REVERT: G 23 ILE cc_start: 0.8891 (mm) cc_final: 0.8639 (mp) REVERT: G 139 ARG cc_start: 0.7522 (ttt-90) cc_final: 0.7224 (ttp80) REVERT: G 181 LEU cc_start: 0.8539 (tt) cc_final: 0.8275 (tt) REVERT: G 414 ASN cc_start: 0.7933 (p0) cc_final: 0.7683 (p0) outliers start: 103 outliers final: 59 residues processed: 530 average time/residue: 1.1985 time to fit residues: 799.9761 Evaluate side-chains 529 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 461 time to evaluate : 4.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 262 ARG Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 191 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 708 TYR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain E residue 680 MET Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 210 LEU Chi-restraints excluded: chain F residue 416 VAL Chi-restraints excluded: chain F residue 444 LEU Chi-restraints excluded: chain F residue 651 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 167 ILE Chi-restraints excluded: chain G residue 183 ASN Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 541 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 136 ASP Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 408 ASN Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 606 TYR Chi-restraints excluded: chain H residue 704 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 1.9990 chunk 437 optimal weight: 2.9990 chunk 399 optimal weight: 3.9990 chunk 425 optimal weight: 0.8980 chunk 256 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 334 optimal weight: 0.0870 chunk 130 optimal weight: 0.8980 chunk 384 optimal weight: 1.9990 chunk 402 optimal weight: 2.9990 chunk 424 optimal weight: 4.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 ASN D 351 GLN ** D 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37565 Z= 0.209 Angle : 0.633 13.142 50848 Z= 0.311 Chirality : 0.045 0.328 6028 Planarity : 0.004 0.068 6509 Dihedral : 4.224 49.559 5112 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.94 % Allowed : 16.37 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 1.13 (0.12), residues: 4708 helix: 1.99 (0.11), residues: 2390 sheet: 0.69 (0.19), residues: 683 loop : -1.14 (0.14), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 631 HIS 0.004 0.000 HIS D 710 PHE 0.040 0.001 PHE D 273 TYR 0.019 0.001 TYR D 388 ARG 0.020 0.000 ARG A 282 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 487 time to evaluate : 4.323 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 23 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8905 (mp) REVERT: A 193 GLU cc_start: 0.7596 (tm-30) cc_final: 0.6683 (tm-30) REVERT: A 195 ASP cc_start: 0.8538 (t0) cc_final: 0.8133 (t0) REVERT: A 210 LEU cc_start: 0.8354 (mm) cc_final: 0.7783 (tp) REVERT: A 323 ASN cc_start: 0.8415 (t0) cc_final: 0.7997 (t0) REVERT: A 376 ARG cc_start: 0.7332 (ptp-110) cc_final: 0.7093 (ptp-110) REVERT: A 394 ARG cc_start: 0.8483 (mtp85) cc_final: 0.7733 (ttp-110) REVERT: A 398 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8498 (pp) REVERT: A 444 LEU cc_start: 0.8614 (mp) cc_final: 0.8414 (mt) REVERT: B 124 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7899 (pp) REVERT: B 136 ASP cc_start: 0.7533 (t70) cc_final: 0.7273 (t0) REVERT: B 137 ILE cc_start: 0.8582 (mt) cc_final: 0.8197 (mp) REVERT: B 195 ASP cc_start: 0.8716 (t70) cc_final: 0.8347 (t0) REVERT: C 164 ASN cc_start: 0.8414 (p0) cc_final: 0.8127 (p0) REVERT: C 189 LEU cc_start: 0.8736 (tt) cc_final: 0.8535 (tt) REVERT: C 452 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7150 (ptt-90) REVERT: D 144 ASP cc_start: 0.8354 (t0) cc_final: 0.8111 (t0) REVERT: D 225 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7452 (pt) REVERT: D 394 ARG cc_start: 0.7746 (OUTLIER) cc_final: 0.7456 (mtp180) REVERT: E 139 ARG cc_start: 0.7906 (tpt170) cc_final: 0.7496 (ttp80) REVERT: E 408 ASN cc_start: 0.4918 (t0) cc_final: 0.4713 (t0) REVERT: E 680 MET cc_start: 0.8591 (mtm) cc_final: 0.8362 (mtt) REVERT: F 103 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8521 (mp) REVERT: F 210 LEU cc_start: 0.8194 (mm) cc_final: 0.7636 (tp) REVERT: F 651 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8456 (m-30) REVERT: F 680 MET cc_start: 0.8375 (mtm) cc_final: 0.8162 (mmm) REVERT: G 23 ILE cc_start: 0.8873 (mm) cc_final: 0.8636 (mp) REVERT: G 139 ARG cc_start: 0.7475 (ttt-90) cc_final: 0.7210 (ttp80) REVERT: G 181 LEU cc_start: 0.8567 (tt) cc_final: 0.8311 (tt) REVERT: G 414 ASN cc_start: 0.7853 (p0) cc_final: 0.7618 (p0) REVERT: G 681 LYS cc_start: 0.8585 (mttt) cc_final: 0.8378 (mtmp) REVERT: H 127 LEU cc_start: 0.8895 (mm) cc_final: 0.8626 (mm) REVERT: H 190 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8043 (tm) outliers start: 79 outliers final: 53 residues processed: 531 average time/residue: 1.1627 time to fit residues: 776.7576 Evaluate side-chains 525 residues out of total 4075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 463 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 543 ILE Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 152 THR Chi-restraints excluded: chain B residue 158 THR Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 194 ILE Chi-restraints excluded: chain B residue 447 PHE Chi-restraints excluded: chain B residue 669 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 113 GLU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 235 THR Chi-restraints excluded: chain C residue 428 ILE Chi-restraints excluded: chain C residue 452 ARG Chi-restraints excluded: chain C residue 456 GLU Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 708 TYR Chi-restraints excluded: chain D residue 222 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 234 LEU Chi-restraints excluded: chain D residue 284 GLU Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 348 GLU Chi-restraints excluded: chain D residue 394 ARG Chi-restraints excluded: chain D residue 474 ILE Chi-restraints excluded: chain D residue 605 ASP Chi-restraints excluded: chain D residue 708 TYR Chi-restraints excluded: chain E residue 23 ILE Chi-restraints excluded: chain E residue 58 ASP Chi-restraints excluded: chain E residue 214 SER Chi-restraints excluded: chain E residue 541 THR Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 124 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 541 THR Chi-restraints excluded: chain F residue 651 ASP Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 234 LEU Chi-restraints excluded: chain G residue 428 ILE Chi-restraints excluded: chain G residue 432 ILE Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 541 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 109 GLN Chi-restraints excluded: chain H residue 190 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 228 ASP Chi-restraints excluded: chain H residue 408 ASN Chi-restraints excluded: chain H residue 436 LEU Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 704 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 279 optimal weight: 0.5980 chunk 450 optimal weight: 2.9990 chunk 274 optimal weight: 0.6980 chunk 213 optimal weight: 2.9990 chunk 312 optimal weight: 8.9990 chunk 472 optimal weight: 2.9990 chunk 434 optimal weight: 0.8980 chunk 376 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 230 optimal weight: 0.2980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: