Starting phenix.real_space_refine on Tue Feb 20 06:23:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oku_20105/02_2024/6oku_20105.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oku_20105/02_2024/6oku_20105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oku_20105/02_2024/6oku_20105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oku_20105/02_2024/6oku_20105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oku_20105/02_2024/6oku_20105.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oku_20105/02_2024/6oku_20105.pdb" } resolution = 3.8 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= 0.001 sd= 0.006 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 42 5.16 5 C 16926 2.51 5 N 4368 2.21 5 O 5712 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 232": "NH1" <-> "NH2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 282": "OD1" <-> "OD2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 437": "OD1" <-> "OD2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 701": "OE1" <-> "OE2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 712": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 282": "OD1" <-> "OD2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 437": "OD1" <-> "OD2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 540": "OD1" <-> "OD2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ARG 607": "NH1" <-> "NH2" Residue "B TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 701": "OE1" <-> "OE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 712": "OE1" <-> "OE2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 282": "OD1" <-> "OD2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "C TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 437": "OD1" <-> "OD2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 540": "OD1" <-> "OD2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ARG 607": "NH1" <-> "NH2" Residue "C TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 701": "OE1" <-> "OE2" Residue "C TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 712": "OE1" <-> "OE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 282": "OD1" <-> "OD2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 437": "OD1" <-> "OD2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 540": "OD1" <-> "OD2" Residue "D ASP 568": "OD1" <-> "OD2" Residue "D ARG 607": "NH1" <-> "NH2" Residue "D TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 701": "OE1" <-> "OE2" Residue "D TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 712": "OE1" <-> "OE2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 282": "OD1" <-> "OD2" Residue "E ARG 290": "NH1" <-> "NH2" Residue "E ARG 325": "NH1" <-> "NH2" Residue "E TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 437": "OD1" <-> "OD2" Residue "E PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 540": "OD1" <-> "OD2" Residue "E ASP 568": "OD1" <-> "OD2" Residue "E ARG 607": "NH1" <-> "NH2" Residue "E TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 701": "OE1" <-> "OE2" Residue "E TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 712": "OE1" <-> "OE2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 282": "OD1" <-> "OD2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 325": "NH1" <-> "NH2" Residue "F TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 437": "OD1" <-> "OD2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 540": "OD1" <-> "OD2" Residue "F ASP 568": "OD1" <-> "OD2" Residue "F ARG 607": "NH1" <-> "NH2" Residue "F TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 701": "OE1" <-> "OE2" Residue "F TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 712": "OE1" <-> "OE2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 282": "OD1" <-> "OD2" Residue "G ARG 290": "NH1" <-> "NH2" Residue "G ARG 325": "NH1" <-> "NH2" Residue "G TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 437": "OD1" <-> "OD2" Residue "G PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 540": "OD1" <-> "OD2" Residue "G ASP 568": "OD1" <-> "OD2" Residue "G ARG 607": "NH1" <-> "NH2" Residue "G TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 701": "OE1" <-> "OE2" Residue "G TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 712": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27048 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "B" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "C" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "D" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "E" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "F" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Chain: "G" Number of atoms: 3864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3864 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 472} Chain breaks: 1 Time building chain proxies: 13.35, per 1000 atoms: 0.49 Number of scatterers: 27048 At special positions: 0 Unit cell: (182.7, 179.8, 134.85, 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 42 16.00 O 5712 8.00 N 4368 7.00 C 16926 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: 9.69 Conformation dependent library (CDL) restraints added in 5.0 seconds 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6468 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 64 sheets defined 13.8% alpha, 33.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.31 Creating SS restraints... Processing helix chain 'A' and resid 226 through 232 Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.689A pdb=" N SER A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 503 through 505 No H-bonds generated for 'chain 'A' and resid 503 through 505' Processing helix chain 'A' and resid 506 through 513 removed outlier: 3.854A pdb=" N ILE A 510 " --> pdb=" O TYR A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 removed outlier: 3.659A pdb=" N PHE A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 593 removed outlier: 3.600A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.603A pdb=" N VAL A 603 " --> pdb=" O ILE A 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 232 Processing helix chain 'B' and resid 272 through 278 removed outlier: 3.688A pdb=" N SER B 278 " --> pdb=" O TYR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'B' and resid 506 through 513 removed outlier: 3.853A pdb=" N ILE B 510 " --> pdb=" O TYR B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 removed outlier: 3.660A pdb=" N PHE B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 593 removed outlier: 3.601A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 removed outlier: 3.602A pdb=" N VAL B 603 " --> pdb=" O ILE B 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 232 Processing helix chain 'C' and resid 272 through 278 removed outlier: 3.688A pdb=" N SER C 278 " --> pdb=" O TYR C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 506 through 513 removed outlier: 3.854A pdb=" N ILE C 510 " --> pdb=" O TYR C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 removed outlier: 3.659A pdb=" N PHE C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 593 removed outlier: 3.601A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.603A pdb=" N VAL C 603 " --> pdb=" O ILE C 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 232 Processing helix chain 'D' and resid 272 through 278 removed outlier: 3.688A pdb=" N SER D 278 " --> pdb=" O TYR D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 503 through 505 No H-bonds generated for 'chain 'D' and resid 503 through 505' Processing helix chain 'D' and resid 506 through 513 removed outlier: 3.853A pdb=" N ILE D 510 " --> pdb=" O TYR D 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 removed outlier: 3.659A pdb=" N PHE D 555 " --> pdb=" O ILE D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 593 removed outlier: 3.601A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 removed outlier: 3.602A pdb=" N VAL D 603 " --> pdb=" O ILE D 600 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'E' and resid 272 through 278 removed outlier: 3.688A pdb=" N SER E 278 " --> pdb=" O TYR E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 503 through 505 No H-bonds generated for 'chain 'E' and resid 503 through 505' Processing helix chain 'E' and resid 506 through 513 removed outlier: 3.854A pdb=" N ILE E 510 " --> pdb=" O TYR E 506 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 555 removed outlier: 3.660A pdb=" N PHE E 555 " --> pdb=" O ILE E 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 593 removed outlier: 3.601A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 removed outlier: 3.603A pdb=" N VAL E 603 " --> pdb=" O ILE E 600 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 232 Processing helix chain 'F' and resid 272 through 278 removed outlier: 3.688A pdb=" N SER F 278 " --> pdb=" O TYR F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 503 through 505 No H-bonds generated for 'chain 'F' and resid 503 through 505' Processing helix chain 'F' and resid 506 through 513 removed outlier: 3.854A pdb=" N ILE F 510 " --> pdb=" O TYR F 506 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 555 removed outlier: 3.659A pdb=" N PHE F 555 " --> pdb=" O ILE F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 593 removed outlier: 3.601A pdb=" N LYS F 593 " --> pdb=" O LYS F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 removed outlier: 3.603A pdb=" N VAL F 603 " --> pdb=" O ILE F 600 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 232 Processing helix chain 'G' and resid 272 through 278 removed outlier: 3.687A pdb=" N SER G 278 " --> pdb=" O TYR G 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 290 Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 503 through 505 No H-bonds generated for 'chain 'G' and resid 503 through 505' Processing helix chain 'G' and resid 506 through 513 removed outlier: 3.854A pdb=" N ILE G 510 " --> pdb=" O TYR G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 555 removed outlier: 3.659A pdb=" N PHE G 555 " --> pdb=" O ILE G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 593 removed outlier: 3.600A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 removed outlier: 3.603A pdb=" N VAL G 603 " --> pdb=" O ILE G 600 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL A 300 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR A 398 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL A 300 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR A 398 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL A 302 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR A 396 " --> pdb=" O VAL A 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET A 304 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG A 394 " --> pdb=" O MET A 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 306 " --> pdb=" O ASN A 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 314 through 326 removed outlier: 3.729A pdb=" N ASN A 371 " --> pdb=" O ARG B 325 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ASN B 371 " --> pdb=" O ARG C 325 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN C 371 " --> pdb=" O ARG D 325 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASN D 371 " --> pdb=" O ARG E 325 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASN E 371 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN F 371 " --> pdb=" O ARG G 325 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASN G 371 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL A 406 " --> pdb=" O SER A 484 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER A 484 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 482 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.536A pdb=" N THR A 489 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 525 through 531 Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU A 564 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR A 618 " --> pdb=" O ILE A 738 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR A 680 " --> pdb=" O SER A 728 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 695 " --> pdb=" O SER A 683 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL B 300 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR B 398 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL B 300 " --> pdb=" O THR B 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR B 398 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL B 302 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR B 396 " --> pdb=" O VAL B 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET B 304 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG B 394 " --> pdb=" O MET B 304 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS B 306 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.610A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL B 406 " --> pdb=" O SER B 484 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER B 484 " --> pdb=" O VAL B 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN B 482 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 489 through 490 removed outlier: 3.536A pdb=" N THR B 489 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 525 through 531 Processing sheet with id=AB8, first strand: chain 'B' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU B 564 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR B 618 " --> pdb=" O ILE B 738 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR B 680 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR B 695 " --> pdb=" O SER B 683 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC3, first strand: chain 'C' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL C 300 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR C 398 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL C 302 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR C 396 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET C 304 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG C 394 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL C 300 " --> pdb=" O THR C 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR C 398 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL C 302 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR C 396 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET C 304 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG C 394 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL C 406 " --> pdb=" O SER C 484 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER C 484 " --> pdb=" O VAL C 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN C 482 " --> pdb=" O PRO C 408 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 489 through 490 removed outlier: 3.536A pdb=" N THR C 489 " --> pdb=" O VAL C 497 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 525 through 531 Processing sheet with id=AC8, first strand: chain 'C' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU C 564 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR C 618 " --> pdb=" O ILE C 738 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR C 680 " --> pdb=" O SER C 728 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR C 695 " --> pdb=" O SER C 683 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AD3, first strand: chain 'D' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL D 300 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR D 398 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL D 300 " --> pdb=" O THR D 398 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N THR D 398 " --> pdb=" O VAL D 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL D 406 " --> pdb=" O SER D 484 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER D 484 " --> pdb=" O VAL D 406 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN D 482 " --> pdb=" O PRO D 408 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 489 through 490 removed outlier: 3.536A pdb=" N THR D 489 " --> pdb=" O VAL D 497 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 525 through 531 Processing sheet with id=AD8, first strand: chain 'D' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU D 564 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 618 through 619 removed outlier: 3.548A pdb=" N TYR D 618 " --> pdb=" O ILE D 738 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 651 through 659 removed outlier: 4.178A pdb=" N THR D 680 " --> pdb=" O SER D 728 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR D 695 " --> pdb=" O SER D 683 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AE3, first strand: chain 'E' and resid 299 through 311 removed outlier: 5.377A pdb=" N VAL E 300 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR E 398 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 299 through 311 removed outlier: 5.377A pdb=" N VAL E 300 " --> pdb=" O THR E 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR E 398 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL E 406 " --> pdb=" O SER E 484 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N SER E 484 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN E 482 " --> pdb=" O PRO E 408 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 489 through 490 removed outlier: 3.535A pdb=" N THR E 489 " --> pdb=" O VAL E 497 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'E' and resid 525 through 531 Processing sheet with id=AE8, first strand: chain 'E' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU E 564 " --> pdb=" O ILE E 571 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR E 618 " --> pdb=" O ILE E 738 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR E 680 " --> pdb=" O SER E 728 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR E 695 " --> pdb=" O SER E 683 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AF3, first strand: chain 'F' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL F 300 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR F 398 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL F 302 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR F 396 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET F 304 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG F 394 " --> pdb=" O MET F 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS F 306 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 299 through 311 removed outlier: 5.378A pdb=" N VAL F 300 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR F 398 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N VAL F 302 " --> pdb=" O TYR F 396 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TYR F 396 " --> pdb=" O VAL F 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET F 304 " --> pdb=" O ARG F 394 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG F 394 " --> pdb=" O MET F 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS F 306 " --> pdb=" O ASN F 392 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL F 406 " --> pdb=" O SER F 484 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER F 484 " --> pdb=" O VAL F 406 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN F 482 " --> pdb=" O PRO F 408 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 489 through 490 removed outlier: 3.536A pdb=" N THR F 489 " --> pdb=" O VAL F 497 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 525 through 531 Processing sheet with id=AF8, first strand: chain 'F' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU F 564 " --> pdb=" O ILE F 571 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR F 618 " --> pdb=" O ILE F 738 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR F 680 " --> pdb=" O SER F 728 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR F 695 " --> pdb=" O SER F 683 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AG3, first strand: chain 'G' and resid 299 through 311 removed outlier: 5.377A pdb=" N VAL G 300 " --> pdb=" O THR G 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR G 398 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL G 302 " --> pdb=" O TYR G 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR G 396 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET G 304 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG G 394 " --> pdb=" O MET G 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS G 306 " --> pdb=" O ASN G 392 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 299 through 311 removed outlier: 5.377A pdb=" N VAL G 300 " --> pdb=" O THR G 398 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR G 398 " --> pdb=" O VAL G 300 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL G 302 " --> pdb=" O TYR G 396 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N TYR G 396 " --> pdb=" O VAL G 302 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N MET G 304 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ARG G 394 " --> pdb=" O MET G 304 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS G 306 " --> pdb=" O ASN G 392 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.611A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N VAL G 406 " --> pdb=" O SER G 484 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N SER G 484 " --> pdb=" O VAL G 406 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN G 482 " --> pdb=" O PRO G 408 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 489 through 490 removed outlier: 3.535A pdb=" N THR G 489 " --> pdb=" O VAL G 497 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 525 through 531 Processing sheet with id=AG8, first strand: chain 'G' and resid 558 through 560 removed outlier: 3.741A pdb=" N LEU G 564 " --> pdb=" O ILE G 571 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'G' and resid 618 through 619 removed outlier: 3.549A pdb=" N TYR G 618 " --> pdb=" O ILE G 738 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'G' and resid 651 through 659 removed outlier: 4.179A pdb=" N THR G 680 " --> pdb=" O SER G 728 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR G 695 " --> pdb=" O SER G 683 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.53 Time building geometry restraints manager: 10.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8774 1.34 - 1.45: 4193 1.45 - 1.57: 14473 1.57 - 1.69: 0 1.69 - 1.80: 77 Bond restraints: 27517 Sorted by residual: bond pdb=" C LYS A 541 " pdb=" N THR A 542 " ideal model delta sigma weight residual 1.331 1.295 0.035 1.24e-02 6.50e+03 8.16e+00 bond pdb=" C LYS B 541 " pdb=" N THR B 542 " ideal model delta sigma weight residual 1.331 1.295 0.035 1.24e-02 6.50e+03 8.13e+00 bond pdb=" C LYS D 541 " pdb=" N THR D 542 " ideal model delta sigma weight residual 1.331 1.295 0.035 1.24e-02 6.50e+03 8.08e+00 bond pdb=" C LYS F 541 " pdb=" N THR F 542 " ideal model delta sigma weight residual 1.331 1.296 0.035 1.24e-02 6.50e+03 7.92e+00 bond pdb=" C LYS G 541 " pdb=" N THR G 542 " ideal model delta sigma weight residual 1.331 1.296 0.034 1.24e-02 6.50e+03 7.64e+00 ... (remaining 27512 not shown) Histogram of bond angle deviations from ideal: 99.04 - 106.15: 550 106.15 - 113.25: 15082 113.25 - 120.36: 10262 120.36 - 127.46: 11242 127.46 - 134.57: 181 Bond angle restraints: 37317 Sorted by residual: angle pdb=" CA LEU B 698 " pdb=" CB LEU B 698 " pdb=" CG LEU B 698 " ideal model delta sigma weight residual 116.30 134.57 -18.27 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU D 698 " pdb=" CB LEU D 698 " pdb=" CG LEU D 698 " ideal model delta sigma weight residual 116.30 134.56 -18.26 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU A 698 " pdb=" CB LEU A 698 " pdb=" CG LEU A 698 " ideal model delta sigma weight residual 116.30 134.56 -18.26 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU E 698 " pdb=" CB LEU E 698 " pdb=" CG LEU E 698 " ideal model delta sigma weight residual 116.30 134.54 -18.24 3.50e+00 8.16e-02 2.72e+01 angle pdb=" CA LEU C 698 " pdb=" CB LEU C 698 " pdb=" CG LEU C 698 " ideal model delta sigma weight residual 116.30 134.53 -18.23 3.50e+00 8.16e-02 2.71e+01 ... (remaining 37312 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 14609 16.99 - 33.98: 1624 33.98 - 50.97: 413 50.97 - 67.96: 84 67.96 - 84.95: 35 Dihedral angle restraints: 16765 sinusoidal: 6664 harmonic: 10101 Sorted by residual: dihedral pdb=" CA TYR F 732 " pdb=" C TYR F 732 " pdb=" N LEU F 733 " pdb=" CA LEU F 733 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA TYR D 732 " pdb=" C TYR D 732 " pdb=" N LEU D 733 " pdb=" CA LEU D 733 " ideal model delta harmonic sigma weight residual 180.00 152.20 27.80 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA TYR C 732 " pdb=" C TYR C 732 " pdb=" N LEU C 733 " pdb=" CA LEU C 733 " ideal model delta harmonic sigma weight residual 180.00 152.20 27.80 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 16762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2549 0.045 - 0.090: 1178 0.090 - 0.135: 389 0.135 - 0.181: 85 0.181 - 0.226: 20 Chirality restraints: 4221 Sorted by residual: chirality pdb=" CB ILE E 547 " pdb=" CA ILE E 547 " pdb=" CG1 ILE E 547 " pdb=" CG2 ILE E 547 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE F 547 " pdb=" CA ILE F 547 " pdb=" CG1 ILE F 547 " pdb=" CG2 ILE F 547 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CB ILE D 547 " pdb=" CA ILE D 547 " pdb=" CG1 ILE D 547 " pdb=" CG2 ILE D 547 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 4218 not shown) Planarity restraints: 4858 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 510 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C ILE E 510 " -0.048 2.00e-02 2.50e+03 pdb=" O ILE E 510 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP E 511 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 510 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.52e+00 pdb=" C ILE D 510 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE D 510 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP D 511 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 510 " 0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C ILE F 510 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE F 510 " 0.018 2.00e-02 2.50e+03 pdb=" N ASP F 511 " 0.016 2.00e-02 2.50e+03 ... (remaining 4855 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 3144 2.74 - 3.28: 25374 3.28 - 3.82: 43397 3.82 - 4.36: 46765 4.36 - 4.90: 84221 Nonbonded interactions: 202901 Sorted by model distance: nonbonded pdb=" OG1 THR A 638 " pdb=" OD1 ASN A 648 " model vdw 2.202 2.440 nonbonded pdb=" OG1 THR E 638 " pdb=" OD1 ASN E 648 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR C 638 " pdb=" OD1 ASN C 648 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR F 638 " pdb=" OD1 ASN F 648 " model vdw 2.203 2.440 nonbonded pdb=" OG1 THR D 638 " pdb=" OD1 ASN D 648 " model vdw 2.203 2.440 ... (remaining 202896 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 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: 0.010 Extract box with map and model: 4.790 Check model and map are aligned: 0.370 Set scattering table: 0.210 Process input model: 67.700 Find NCS groups from input model: 1.790 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: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.007 0.062 27517 Z= 0.484 Angle : 1.008 18.269 37317 Z= 0.555 Chirality : 0.057 0.226 4221 Planarity : 0.006 0.060 4858 Dihedral : 15.775 84.946 10297 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 2.97 % Allowed : 8.68 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -4.09 (0.12), residues: 3423 helix: -3.76 (0.13), residues: 448 sheet: -1.00 (0.16), residues: 1008 loop : -3.58 (0.11), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 375 HIS 0.008 0.005 HIS A 314 PHE 0.032 0.004 PHE A 281 TYR 0.019 0.002 TYR B 261 ARG 0.004 0.001 ARG F 458 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 232 time to evaluate : 3.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.7186 (m-10) cc_final: 0.6167 (m-10) REVERT: A 379 LEU cc_start: 0.8511 (tt) cc_final: 0.8122 (mp) REVERT: A 400 THR cc_start: 0.9197 (OUTLIER) cc_final: 0.8748 (p) REVERT: A 707 PHE cc_start: 0.8155 (p90) cc_final: 0.7485 (p90) REVERT: A 741 LEU cc_start: 0.7717 (tp) cc_final: 0.7358 (tp) REVERT: B 417 ASP cc_start: 0.7471 (p0) cc_final: 0.7139 (p0) REVERT: B 707 PHE cc_start: 0.7876 (p90) cc_final: 0.7639 (p90) REVERT: C 313 GLU cc_start: 0.6366 (mm-30) cc_final: 0.6132 (mm-30) REVERT: D 707 PHE cc_start: 0.8276 (p90) cc_final: 0.7719 (p90) REVERT: E 313 GLU cc_start: 0.7271 (mm-30) cc_final: 0.7009 (mm-30) REVERT: E 314 HIS cc_start: 0.7160 (m-70) cc_final: 0.6903 (m90) REVERT: E 379 LEU cc_start: 0.8330 (tt) cc_final: 0.7875 (mp) REVERT: E 400 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8667 (p) REVERT: E 403 MET cc_start: 0.8450 (tpt) cc_final: 0.8239 (tpp) REVERT: E 417 ASP cc_start: 0.7554 (p0) cc_final: 0.7275 (p0) REVERT: F 379 LEU cc_start: 0.8246 (tt) cc_final: 0.7979 (mp) REVERT: F 537 ASP cc_start: 0.8398 (t70) cc_final: 0.8021 (t0) REVERT: F 707 PHE cc_start: 0.8268 (p90) cc_final: 0.7953 (p90) REVERT: G 230 TYR cc_start: 0.6789 (m-10) cc_final: 0.5891 (m-80) REVERT: G 495 GLN cc_start: 0.7851 (pm20) cc_final: 0.7643 (pm20) REVERT: G 707 PHE cc_start: 0.8246 (p90) cc_final: 0.7934 (p90) outliers start: 91 outliers final: 37 residues processed: 302 average time/residue: 0.3800 time to fit residues: 181.4979 Evaluate side-chains 185 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 146 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 655 LYS Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 686 VAL Chi-restraints excluded: chain B residue 688 ILE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 688 ILE Chi-restraints excluded: chain C residue 718 SER Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 688 ILE Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 688 ILE Chi-restraints excluded: chain E residue 718 SER Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 688 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 688 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 10.0000 chunk 259 optimal weight: 0.9990 chunk 144 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 268 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 chunk 311 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 GLN ** A 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN B 252 GLN B 431 ASN C 252 GLN C 431 ASN D 252 GLN D 431 ASN E 252 GLN ** E 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 431 ASN F 252 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 252 GLN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 431 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 27517 Z= 0.189 Angle : 0.590 12.994 37317 Z= 0.310 Chirality : 0.044 0.174 4221 Planarity : 0.004 0.042 4858 Dihedral : 6.365 54.224 3748 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.55 % Favored : 90.45 % Rotamer: Outliers : 2.35 % Allowed : 13.57 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.46 (0.13), residues: 3423 helix: -2.56 (0.18), residues: 462 sheet: -0.83 (0.16), residues: 1008 loop : -3.20 (0.12), residues: 1953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 375 HIS 0.002 0.001 HIS E 314 PHE 0.016 0.002 PHE G 281 TYR 0.013 0.001 TYR E 697 ARG 0.002 0.000 ARG F 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 171 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 TYR cc_start: 0.6898 (m-10) cc_final: 0.6537 (m-80) REVERT: A 660 MET cc_start: 0.7533 (mmm) cc_final: 0.7147 (ttt) REVERT: A 707 PHE cc_start: 0.8141 (p90) cc_final: 0.7590 (p90) REVERT: B 644 GLN cc_start: 0.6242 (OUTLIER) cc_final: 0.5753 (pm20) REVERT: B 660 MET cc_start: 0.7304 (mmm) cc_final: 0.7048 (ttt) REVERT: B 692 GLU cc_start: 0.5736 (OUTLIER) cc_final: 0.5390 (mp0) REVERT: B 707 PHE cc_start: 0.8025 (p90) cc_final: 0.7709 (p90) REVERT: C 230 TYR cc_start: 0.6591 (m-10) cc_final: 0.6363 (m-80) REVERT: C 538 PRO cc_start: 0.9010 (Cg_endo) cc_final: 0.8658 (Cg_exo) REVERT: C 660 MET cc_start: 0.7672 (mmm) cc_final: 0.7275 (ttm) REVERT: D 230 TYR cc_start: 0.7058 (m-10) cc_final: 0.6759 (m-80) REVERT: D 453 ASP cc_start: 0.7828 (t0) cc_final: 0.7624 (m-30) REVERT: D 644 GLN cc_start: 0.5887 (OUTLIER) cc_final: 0.5504 (pm20) REVERT: D 707 PHE cc_start: 0.8095 (p90) cc_final: 0.7447 (p90) REVERT: F 644 GLN cc_start: 0.5476 (OUTLIER) cc_final: 0.5083 (pm20) REVERT: F 707 PHE cc_start: 0.8421 (p90) cc_final: 0.7899 (p90) REVERT: G 453 ASP cc_start: 0.8037 (t0) cc_final: 0.7825 (m-30) REVERT: G 644 GLN cc_start: 0.6610 (OUTLIER) cc_final: 0.6259 (pm20) REVERT: G 660 MET cc_start: 0.7608 (mmm) cc_final: 0.7229 (ttt) REVERT: G 707 PHE cc_start: 0.8324 (p90) cc_final: 0.7865 (p90) outliers start: 72 outliers final: 54 residues processed: 229 average time/residue: 0.3962 time to fit residues: 143.5168 Evaluate side-chains 188 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 129 time to evaluate : 3.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 644 GLN Chi-restraints excluded: chain F residue 685 ILE Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 692 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 173 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 259 optimal weight: 1.9990 chunk 212 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 312 optimal weight: 0.0370 chunk 337 optimal weight: 0.0970 chunk 277 optimal weight: 8.9990 chunk 309 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 overall best weight: 2.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 735 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 27517 Z= 0.203 Angle : 0.598 14.350 37317 Z= 0.304 Chirality : 0.043 0.161 4221 Planarity : 0.004 0.043 4858 Dihedral : 5.933 44.671 3721 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 4.01 % Allowed : 15.69 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -3.10 (0.13), residues: 3423 helix: -1.88 (0.21), residues: 462 sheet: -0.56 (0.16), residues: 938 loop : -3.01 (0.12), residues: 2023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 375 HIS 0.002 0.001 HIS G 314 PHE 0.016 0.002 PHE E 281 TYR 0.029 0.001 TYR F 230 ARG 0.002 0.000 ARG B 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 142 time to evaluate : 3.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.6894 (p90) REVERT: A 660 MET cc_start: 0.7562 (mmm) cc_final: 0.7033 (ttt) REVERT: A 707 PHE cc_start: 0.8085 (p90) cc_final: 0.7490 (p90) REVERT: B 281 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7171 (p90) REVERT: B 644 GLN cc_start: 0.6154 (OUTLIER) cc_final: 0.5614 (pm20) REVERT: B 692 GLU cc_start: 0.5651 (OUTLIER) cc_final: 0.5335 (mp0) REVERT: B 707 PHE cc_start: 0.8021 (p90) cc_final: 0.7658 (p90) REVERT: C 281 PHE cc_start: 0.7553 (OUTLIER) cc_final: 0.6393 (p90) REVERT: C 538 PRO cc_start: 0.9036 (Cg_endo) cc_final: 0.8700 (Cg_exo) REVERT: C 663 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8320 (mt) REVERT: C 664 LYS cc_start: 0.8918 (mmmt) cc_final: 0.8609 (tppt) REVERT: D 281 PHE cc_start: 0.7973 (OUTLIER) cc_final: 0.7002 (p90) REVERT: D 644 GLN cc_start: 0.5707 (OUTLIER) cc_final: 0.5279 (pm20) REVERT: D 663 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8364 (mt) REVERT: D 707 PHE cc_start: 0.7990 (p90) cc_final: 0.7399 (p90) REVERT: E 281 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.6956 (p90) REVERT: E 644 GLN cc_start: 0.5956 (OUTLIER) cc_final: 0.5602 (pm20) REVERT: E 663 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8585 (mt) REVERT: F 281 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7137 (p90) REVERT: F 644 GLN cc_start: 0.5427 (OUTLIER) cc_final: 0.5073 (pm20) REVERT: F 707 PHE cc_start: 0.8389 (p90) cc_final: 0.7795 (p90) REVERT: G 281 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7363 (p90) REVERT: G 644 GLN cc_start: 0.6578 (OUTLIER) cc_final: 0.6288 (pm20) REVERT: G 660 MET cc_start: 0.7316 (mmm) cc_final: 0.7079 (ttt) REVERT: G 707 PHE cc_start: 0.8272 (p90) cc_final: 0.7761 (p90) outliers start: 123 outliers final: 76 residues processed: 246 average time/residue: 0.3371 time to fit residues: 138.1849 Evaluate side-chains 218 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 126 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 644 GLN Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 692 GLU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 644 GLN Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 GLN Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 644 GLN Chi-restraints excluded: chain F residue 685 ILE Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 698 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 308 optimal weight: 7.9990 chunk 234 optimal weight: 0.0030 chunk 161 optimal weight: 3.9990 chunk 34 optimal weight: 5.9990 chunk 148 optimal weight: 8.9990 chunk 209 optimal weight: 5.9990 chunk 313 optimal weight: 10.0000 chunk 331 optimal weight: 0.6980 chunk 163 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 overall best weight: 2.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN D 427 ASN D 432 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** G 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 27517 Z= 0.237 Angle : 0.608 15.638 37317 Z= 0.310 Chirality : 0.044 0.155 4221 Planarity : 0.004 0.044 4858 Dihedral : 6.037 49.780 3721 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 4.92 % Allowed : 16.50 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.82 (0.13), residues: 3423 helix: -1.67 (0.21), residues: 476 sheet: -0.47 (0.16), residues: 1036 loop : -2.86 (0.13), residues: 1911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 375 HIS 0.002 0.001 HIS G 314 PHE 0.019 0.002 PHE B 281 TYR 0.023 0.001 TYR B 230 ARG 0.003 0.000 ARG F 528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 129 time to evaluate : 3.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7042 (p90) REVERT: A 660 MET cc_start: 0.7468 (mmm) cc_final: 0.6802 (ttt) REVERT: A 707 PHE cc_start: 0.8098 (p90) cc_final: 0.7496 (p90) REVERT: A 713 THR cc_start: 0.5511 (m) cc_final: 0.5059 (p) REVERT: B 281 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.7076 (p90) REVERT: B 707 PHE cc_start: 0.8065 (p90) cc_final: 0.7659 (p90) REVERT: C 281 PHE cc_start: 0.7451 (OUTLIER) cc_final: 0.6451 (p90) REVERT: C 538 PRO cc_start: 0.9026 (Cg_endo) cc_final: 0.8695 (Cg_exo) REVERT: C 663 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8390 (mt) REVERT: C 664 LYS cc_start: 0.8914 (mmmt) cc_final: 0.8666 (tppt) REVERT: D 281 PHE cc_start: 0.7673 (OUTLIER) cc_final: 0.6962 (p90) REVERT: D 707 PHE cc_start: 0.7995 (p90) cc_final: 0.7394 (p90) REVERT: E 281 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.6932 (p90) REVERT: E 644 GLN cc_start: 0.5943 (OUTLIER) cc_final: 0.5691 (pm20) REVERT: F 281 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7254 (p90) REVERT: F 663 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8497 (mt) REVERT: F 707 PHE cc_start: 0.8388 (p90) cc_final: 0.7789 (p90) REVERT: F 741 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7658 (mm) REVERT: G 281 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7444 (p90) outliers start: 151 outliers final: 101 residues processed: 265 average time/residue: 0.3162 time to fit residues: 143.2737 Evaluate side-chains 231 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 119 time to evaluate : 3.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 644 GLN Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 314 HIS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 505 ASP Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 663 LEU Chi-restraints excluded: chain F residue 685 ILE Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 636 ASN Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 686 VAL Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 276 optimal weight: 6.9990 chunk 188 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 246 optimal weight: 9.9990 chunk 136 optimal weight: 7.9990 chunk 282 optimal weight: 7.9990 chunk 229 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 297 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 432 ASN ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 ASN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 390 ASN D 427 ASN ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 432 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 27517 Z= 0.382 Angle : 0.708 14.868 37317 Z= 0.368 Chirality : 0.046 0.208 4221 Planarity : 0.004 0.046 4858 Dihedral : 6.786 57.558 3721 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.01 % Favored : 87.99 % Rotamer: Outliers : 6.07 % Allowed : 16.70 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.99 (0.13), residues: 3423 helix: -1.72 (0.22), residues: 427 sheet: -0.71 (0.16), residues: 938 loop : -2.82 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 375 HIS 0.003 0.001 HIS D 314 PHE 0.026 0.003 PHE B 281 TYR 0.035 0.002 TYR F 230 ARG 0.004 0.000 ARG F 528 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 117 time to evaluate : 3.105 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 281 PHE cc_start: 0.7442 (OUTLIER) cc_final: 0.6982 (p90) REVERT: A 400 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8627 (p) REVERT: A 660 MET cc_start: 0.7710 (mmm) cc_final: 0.6875 (ttt) REVERT: A 663 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8125 (pp) REVERT: A 713 THR cc_start: 0.5399 (m) cc_final: 0.4690 (p) REVERT: B 281 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7671 (p90) REVERT: B 707 PHE cc_start: 0.8392 (p90) cc_final: 0.7505 (p90) REVERT: C 230 TYR cc_start: 0.6470 (OUTLIER) cc_final: 0.6116 (m-80) REVERT: C 281 PHE cc_start: 0.7733 (OUTLIER) cc_final: 0.6909 (p90) REVERT: C 403 MET cc_start: 0.8136 (tpt) cc_final: 0.7466 (tpt) REVERT: C 538 PRO cc_start: 0.9133 (Cg_endo) cc_final: 0.8841 (Cg_exo) REVERT: C 660 MET cc_start: 0.6514 (ttt) cc_final: 0.5634 (tmm) REVERT: C 663 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8409 (pp) REVERT: C 664 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8580 (tppt) REVERT: D 281 PHE cc_start: 0.7629 (OUTLIER) cc_final: 0.7115 (p90) REVERT: D 379 LEU cc_start: 0.8192 (tt) cc_final: 0.7931 (tp) REVERT: D 537 ASP cc_start: 0.8254 (t70) cc_final: 0.7795 (t0) REVERT: D 664 LYS cc_start: 0.8869 (mmmt) cc_final: 0.8575 (tppt) REVERT: D 707 PHE cc_start: 0.8014 (p90) cc_final: 0.7420 (p90) REVERT: E 281 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7346 (p90) REVERT: E 663 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8484 (mt) REVERT: E 713 THR cc_start: 0.5735 (m) cc_final: 0.5488 (p) REVERT: F 281 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7340 (p90) REVERT: F 707 PHE cc_start: 0.8328 (p90) cc_final: 0.7774 (p90) REVERT: G 281 PHE cc_start: 0.7890 (OUTLIER) cc_final: 0.7398 (p90) REVERT: G 644 GLN cc_start: 0.6434 (OUTLIER) cc_final: 0.6093 (pm20) REVERT: G 663 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8444 (mt) REVERT: G 707 PHE cc_start: 0.8265 (p90) cc_final: 0.7550 (p90) outliers start: 186 outliers final: 140 residues processed: 290 average time/residue: 0.3219 time to fit residues: 158.5582 Evaluate side-chains 263 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 109 time to evaluate : 3.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain C residue 230 TYR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 636 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 314 HIS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 478 LEU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain F residue 505 ASP Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 713 THR Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 636 ASN Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 686 VAL Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 698 LEU Chi-restraints excluded: chain G residue 713 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 111 optimal weight: 5.9990 chunk 298 optimal weight: 0.3980 chunk 65 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 331 optimal weight: 6.9990 chunk 275 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 682 ASN C 223 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 27517 Z= 0.263 Angle : 0.637 14.995 37317 Z= 0.328 Chirality : 0.044 0.180 4221 Planarity : 0.004 0.046 4858 Dihedral : 6.303 56.956 3719 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 5.68 % Allowed : 17.42 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.73 (0.13), residues: 3423 helix: -1.57 (0.22), residues: 434 sheet: -0.51 (0.16), residues: 987 loop : -2.69 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 375 HIS 0.002 0.001 HIS G 314 PHE 0.022 0.002 PHE B 281 TYR 0.027 0.001 TYR B 230 ARG 0.002 0.000 ARG F 528 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 121 time to evaluate : 3.169 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 230 TYR cc_start: 0.6829 (OUTLIER) cc_final: 0.5908 (t80) REVERT: A 281 PHE cc_start: 0.7227 (OUTLIER) cc_final: 0.6877 (p90) REVERT: A 400 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8603 (p) REVERT: A 644 GLN cc_start: 0.6112 (OUTLIER) cc_final: 0.5485 (pm20) REVERT: A 660 MET cc_start: 0.7654 (mmm) cc_final: 0.6846 (ttt) REVERT: A 663 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8089 (pp) REVERT: A 713 THR cc_start: 0.5373 (m) cc_final: 0.4699 (p) REVERT: B 707 PHE cc_start: 0.8310 (p90) cc_final: 0.7623 (p90) REVERT: C 281 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.6883 (p90) REVERT: C 403 MET cc_start: 0.8152 (tpt) cc_final: 0.7645 (tpt) REVERT: C 538 PRO cc_start: 0.9106 (Cg_endo) cc_final: 0.8809 (Cg_exo) REVERT: C 660 MET cc_start: 0.6705 (ttt) cc_final: 0.5594 (tmm) REVERT: C 663 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8505 (pp) REVERT: C 664 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8573 (tppt) REVERT: D 281 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7332 (p90) REVERT: D 537 ASP cc_start: 0.8052 (t70) cc_final: 0.7566 (t0) REVERT: D 707 PHE cc_start: 0.7937 (p90) cc_final: 0.7368 (p90) REVERT: E 281 PHE cc_start: 0.7683 (OUTLIER) cc_final: 0.7132 (p90) REVERT: E 538 PRO cc_start: 0.9082 (Cg_endo) cc_final: 0.8769 (Cg_exo) REVERT: E 643 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6605 (mp) REVERT: F 281 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7457 (p90) REVERT: F 707 PHE cc_start: 0.8267 (p90) cc_final: 0.7732 (p90) REVERT: F 741 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7602 (mm) REVERT: G 281 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7622 (p90) REVERT: G 644 GLN cc_start: 0.6462 (OUTLIER) cc_final: 0.6211 (pm20) REVERT: G 663 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8442 (mt) outliers start: 174 outliers final: 135 residues processed: 281 average time/residue: 0.3111 time to fit residues: 149.1923 Evaluate side-chains 263 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 113 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 732 TYR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 409 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 636 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 409 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 505 ASP Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 643 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 314 HIS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 636 ASN Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 713 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 319 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 189 optimal weight: 6.9990 chunk 242 optimal weight: 4.9990 chunk 187 optimal weight: 10.0000 chunk 279 optimal weight: 5.9990 chunk 185 optimal weight: 5.9990 chunk 330 optimal weight: 7.9990 chunk 206 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 152 optimal weight: 0.6980 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 27517 Z= 0.345 Angle : 0.684 15.211 37317 Z= 0.354 Chirality : 0.045 0.176 4221 Planarity : 0.004 0.047 4858 Dihedral : 6.389 57.090 3719 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.71 % Favored : 88.29 % Rotamer: Outliers : 6.46 % Allowed : 17.22 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.90 (0.13), residues: 3423 helix: -1.64 (0.22), residues: 427 sheet: -0.74 (0.16), residues: 938 loop : -2.71 (0.12), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 375 HIS 0.002 0.001 HIS G 314 PHE 0.029 0.003 PHE B 281 TYR 0.034 0.002 TYR B 230 ARG 0.003 0.000 ARG F 528 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 114 time to evaluate : 3.380 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 230 TYR cc_start: 0.6796 (OUTLIER) cc_final: 0.5821 (t80) REVERT: A 281 PHE cc_start: 0.7409 (OUTLIER) cc_final: 0.6960 (p90) REVERT: A 400 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8625 (p) REVERT: A 660 MET cc_start: 0.7649 (mmm) cc_final: 0.6892 (ttt) REVERT: A 713 THR cc_start: 0.5257 (m) cc_final: 0.4785 (p) REVERT: B 432 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8523 (m-40) REVERT: C 281 PHE cc_start: 0.7752 (OUTLIER) cc_final: 0.7067 (p90) REVERT: C 403 MET cc_start: 0.8031 (tpt) cc_final: 0.7519 (ttt) REVERT: C 538 PRO cc_start: 0.9080 (Cg_endo) cc_final: 0.8800 (Cg_exo) REVERT: C 660 MET cc_start: 0.6686 (ttt) cc_final: 0.5767 (tmm) REVERT: D 537 ASP cc_start: 0.8141 (t70) cc_final: 0.7666 (t0) REVERT: D 707 PHE cc_start: 0.8000 (p90) cc_final: 0.7449 (p90) REVERT: E 281 PHE cc_start: 0.7747 (OUTLIER) cc_final: 0.7308 (p90) REVERT: E 663 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8580 (mt) REVERT: F 281 PHE cc_start: 0.7995 (OUTLIER) cc_final: 0.7402 (p90) REVERT: F 707 PHE cc_start: 0.8304 (p90) cc_final: 0.7788 (p90) REVERT: F 732 TYR cc_start: 0.4727 (OUTLIER) cc_final: 0.3335 (p90) REVERT: F 741 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7506 (mm) REVERT: G 281 PHE cc_start: 0.7817 (OUTLIER) cc_final: 0.7442 (p90) REVERT: G 644 GLN cc_start: 0.6279 (OUTLIER) cc_final: 0.6035 (pm20) REVERT: G 663 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8458 (mt) REVERT: G 707 PHE cc_start: 0.8230 (p90) cc_final: 0.7616 (p90) outliers start: 198 outliers final: 159 residues processed: 290 average time/residue: 0.3155 time to fit residues: 155.6122 Evaluate side-chains 278 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 106 time to evaluate : 3.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 TYR Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 409 THR Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 478 LEU Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 505 ASP Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 732 TYR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 230 TYR Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 ASN Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 460 ILE Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 478 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 631 THR Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 698 LEU Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 409 THR Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 478 LEU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 686 VAL Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 698 LEU Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 422 ILE Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 603 VAL Chi-restraints excluded: chain D residue 636 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 230 TYR Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 422 ILE Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 686 VAL Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 698 LEU Chi-restraints excluded: chain E residue 732 TYR Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 314 HIS Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 409 THR Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 460 ILE Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 502 SER Chi-restraints excluded: chain F residue 505 ASP Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 686 VAL Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 713 THR Chi-restraints excluded: chain F residue 732 TYR Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 409 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 429 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 460 ILE Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 478 LEU Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 545 LEU Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 631 THR Chi-restraints excluded: chain G residue 636 ASN Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 644 GLN Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 713 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 204 optimal weight: 0.0670 chunk 132 optimal weight: 9.9990 chunk 197 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 210 optimal weight: 0.9990 chunk 225 optimal weight: 2.9990 chunk 163 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 300 optimal weight: 0.6980 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 735 ASN C 223 ASN C 735 ASN D 223 ASN D 427 ASN E 621 ASN E 735 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 ASN G 621 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 27517 Z= 0.158 Angle : 0.585 15.273 37317 Z= 0.295 Chirality : 0.043 0.190 4221 Planarity : 0.003 0.044 4858 Dihedral : 5.542 44.602 3717 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer: Outliers : 4.83 % Allowed : 18.75 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.58 (0.13), residues: 3423 helix: -1.22 (0.23), residues: 434 sheet: -0.41 (0.16), residues: 931 loop : -2.60 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 375 HIS 0.002 0.001 HIS A 314 PHE 0.017 0.002 PHE B 281 TYR 0.022 0.001 TYR C 230 ARG 0.001 0.000 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 135 time to evaluate : 3.250 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 281 PHE cc_start: 0.7213 (OUTLIER) cc_final: 0.6922 (p90) REVERT: A 400 THR cc_start: 0.9061 (OUTLIER) cc_final: 0.8548 (p) REVERT: A 660 MET cc_start: 0.7494 (mmm) cc_final: 0.6442 (ttt) REVERT: A 707 PHE cc_start: 0.7672 (p90) cc_final: 0.7355 (p90) REVERT: A 713 THR cc_start: 0.5253 (m) cc_final: 0.4769 (p) REVERT: B 281 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.7003 (p90) REVERT: B 707 PHE cc_start: 0.8200 (p90) cc_final: 0.7588 (p90) REVERT: C 281 PHE cc_start: 0.7341 (OUTLIER) cc_final: 0.6434 (p90) REVERT: C 403 MET cc_start: 0.8247 (tpt) cc_final: 0.7925 (ttt) REVERT: C 538 PRO cc_start: 0.9009 (Cg_endo) cc_final: 0.8708 (Cg_exo) REVERT: D 281 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7277 (p90) REVERT: D 537 ASP cc_start: 0.7945 (t70) cc_final: 0.7522 (t0) REVERT: E 281 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.6982 (p90) REVERT: E 538 PRO cc_start: 0.9032 (Cg_endo) cc_final: 0.8711 (Cg_exo) REVERT: E 663 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8811 (mt) REVERT: F 281 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7057 (p90) REVERT: F 660 MET cc_start: 0.6222 (ttt) cc_final: 0.5358 (tmm) REVERT: F 664 LYS cc_start: 0.9047 (mmmt) cc_final: 0.8837 (tppt) REVERT: F 707 PHE cc_start: 0.8201 (p90) cc_final: 0.7661 (p90) REVERT: F 741 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7464 (mm) REVERT: G 223 ASN cc_start: 0.5581 (OUTLIER) cc_final: 0.5323 (p0) REVERT: G 663 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8471 (mt) outliers start: 148 outliers final: 115 residues processed: 262 average time/residue: 0.3398 time to fit residues: 151.9061 Evaluate side-chains 247 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 121 time to evaluate : 2.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 732 TYR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 692 GLU Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 732 TYR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 460 ILE Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 636 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 663 LEU Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 732 TYR Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 314 HIS Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 505 ASP Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 741 LEU Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 698 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 316 optimal weight: 0.8980 chunk 288 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 185 optimal weight: 0.1980 chunk 134 optimal weight: 0.8980 chunk 241 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 278 optimal weight: 0.7980 chunk 291 optimal weight: 6.9990 chunk 306 optimal weight: 4.9990 chunk 202 optimal weight: 10.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN B 223 ASN B 621 ASN C 223 ASN C 621 ASN C 735 ASN D 621 ASN D 735 ASN E 621 ASN ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 621 ASN ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 621 ASN G 735 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 27517 Z= 0.137 Angle : 0.574 15.577 37317 Z= 0.285 Chirality : 0.043 0.181 4221 Planarity : 0.003 0.039 4858 Dihedral : 5.199 39.370 3713 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.03 % Favored : 90.97 % Rotamer: Outliers : 4.31 % Allowed : 19.34 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.40 (0.14), residues: 3423 helix: -0.84 (0.25), residues: 420 sheet: -0.23 (0.16), residues: 931 loop : -2.56 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 375 HIS 0.002 0.000 HIS G 314 PHE 0.012 0.002 PHE A 281 TYR 0.018 0.001 TYR B 230 ARG 0.002 0.000 ARG G 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 132 time to evaluate : 3.523 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 281 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6719 (p90) REVERT: A 294 VAL cc_start: 0.9351 (OUTLIER) cc_final: 0.9043 (m) REVERT: A 660 MET cc_start: 0.7441 (mmm) cc_final: 0.6599 (ttt) REVERT: A 707 PHE cc_start: 0.7764 (p90) cc_final: 0.7460 (p90) REVERT: C 403 MET cc_start: 0.8179 (tpt) cc_final: 0.7736 (ttt) REVERT: C 538 PRO cc_start: 0.9000 (Cg_endo) cc_final: 0.8692 (Cg_exo) REVERT: C 643 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6444 (tp) REVERT: D 281 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.7157 (p90) REVERT: E 538 PRO cc_start: 0.9021 (Cg_endo) cc_final: 0.8691 (Cg_exo) REVERT: F 660 MET cc_start: 0.6011 (ttt) cc_final: 0.5418 (tmm) REVERT: F 707 PHE cc_start: 0.8215 (p90) cc_final: 0.7670 (p90) REVERT: F 732 TYR cc_start: 0.4246 (OUTLIER) cc_final: 0.3038 (p90) REVERT: G 663 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8382 (mt) REVERT: G 707 PHE cc_start: 0.8276 (p90) cc_final: 0.7749 (p90) outliers start: 132 outliers final: 112 residues processed: 241 average time/residue: 0.3278 time to fit residues: 134.9942 Evaluate side-chains 240 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 122 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 732 TYR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 643 LEU Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 732 TYR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 636 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 732 TYR Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 505 ASP Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 732 TYR Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 389 ILE Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 325 optimal weight: 0.0980 chunk 198 optimal weight: 5.9990 chunk 154 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 341 optimal weight: 20.0000 chunk 314 optimal weight: 1.9990 chunk 272 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 216 optimal weight: 9.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN B 223 ASN B 621 ASN B 735 ASN C 223 ASN C 621 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 735 ASN ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 27517 Z= 0.199 Angle : 0.605 16.351 37317 Z= 0.303 Chirality : 0.043 0.179 4221 Planarity : 0.003 0.041 4858 Dihedral : 5.337 40.555 3713 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 4.27 % Allowed : 19.50 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.42 (0.13), residues: 3423 helix: -0.83 (0.25), residues: 420 sheet: -0.25 (0.16), residues: 917 loop : -2.57 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP E 375 HIS 0.002 0.001 HIS A 314 PHE 0.018 0.002 PHE A 281 TYR 0.028 0.001 TYR B 230 ARG 0.001 0.000 ARG A 668 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6846 Ramachandran restraints generated. 3423 Oldfield, 0 Emsley, 3423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 123 time to evaluate : 3.227 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 281 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6807 (p90) REVERT: A 400 THR cc_start: 0.9118 (OUTLIER) cc_final: 0.8585 (p) REVERT: A 660 MET cc_start: 0.7440 (mmm) cc_final: 0.6638 (ttt) REVERT: A 707 PHE cc_start: 0.8001 (p90) cc_final: 0.7564 (p90) REVERT: B 281 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6954 (p90) REVERT: B 707 PHE cc_start: 0.8228 (p90) cc_final: 0.7646 (p90) REVERT: B 735 ASN cc_start: 0.8554 (m110) cc_final: 0.8311 (m-40) REVERT: C 403 MET cc_start: 0.8161 (tpt) cc_final: 0.7788 (ttt) REVERT: C 538 PRO cc_start: 0.9027 (Cg_endo) cc_final: 0.8723 (Cg_exo) REVERT: D 281 PHE cc_start: 0.7802 (OUTLIER) cc_final: 0.7244 (p90) REVERT: E 538 PRO cc_start: 0.9032 (Cg_endo) cc_final: 0.8701 (Cg_exo) REVERT: F 660 MET cc_start: 0.5997 (ttt) cc_final: 0.5449 (tmm) REVERT: F 707 PHE cc_start: 0.8250 (p90) cc_final: 0.7731 (p90) REVERT: F 732 TYR cc_start: 0.4202 (OUTLIER) cc_final: 0.3055 (p90) REVERT: G 281 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7106 (p90) REVERT: G 663 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8379 (mt) REVERT: G 707 PHE cc_start: 0.8307 (p90) cc_final: 0.7794 (p90) outliers start: 131 outliers final: 117 residues processed: 233 average time/residue: 0.3189 time to fit residues: 127.0459 Evaluate side-chains 245 residues out of total 3066 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 121 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 314 HIS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 400 THR Chi-restraints excluded: chain A residue 410 THR Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 462 ILE Chi-restraints excluded: chain A residue 480 THR Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 631 THR Chi-restraints excluded: chain A residue 636 ASN Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 692 GLU Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 732 TYR Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 403 MET Chi-restraints excluded: chain B residue 409 THR Chi-restraints excluded: chain B residue 422 ILE Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 453 ASP Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 505 ASP Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 636 ASN Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 685 ILE Chi-restraints excluded: chain B residue 733 LEU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 265 ASN Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 314 HIS Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 400 THR Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 460 ILE Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 489 THR Chi-restraints excluded: chain C residue 505 ASP Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 636 ASN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 685 ILE Chi-restraints excluded: chain C residue 732 TYR Chi-restraints excluded: chain C residue 733 LEU Chi-restraints excluded: chain D residue 262 LEU Chi-restraints excluded: chain D residue 271 TYR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 314 HIS Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 400 THR Chi-restraints excluded: chain D residue 429 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 462 ILE Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 636 ASN Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 686 VAL Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 695 THR Chi-restraints excluded: chain D residue 733 LEU Chi-restraints excluded: chain E residue 262 LEU Chi-restraints excluded: chain E residue 314 HIS Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 478 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 502 SER Chi-restraints excluded: chain E residue 545 LEU Chi-restraints excluded: chain E residue 631 THR Chi-restraints excluded: chain E residue 636 ASN Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 692 GLU Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 732 TYR Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 741 LEU Chi-restraints excluded: chain F residue 262 LEU Chi-restraints excluded: chain F residue 294 VAL Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 389 ILE Chi-restraints excluded: chain F residue 429 ILE Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 462 ILE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 505 ASP Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 603 VAL Chi-restraints excluded: chain F residue 631 THR Chi-restraints excluded: chain F residue 636 ASN Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 692 GLU Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 732 TYR Chi-restraints excluded: chain G residue 262 LEU Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 400 THR Chi-restraints excluded: chain G residue 422 ILE Chi-restraints excluded: chain G residue 459 LEU Chi-restraints excluded: chain G residue 462 ILE Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 502 SER Chi-restraints excluded: chain G residue 603 VAL Chi-restraints excluded: chain G residue 636 ASN Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 663 LEU Chi-restraints excluded: chain G residue 692 GLU Chi-restraints excluded: chain G residue 695 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 343 random chunks: chunk 289 optimal weight: 0.0070 chunk 83 optimal weight: 0.6980 chunk 250 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 272 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 279 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 ASN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 621 ASN ** E 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 223 ASN G 427 ASN G 621 ASN ** G 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.108302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.082497 restraints weight = 70787.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.082968 restraints weight = 42977.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.083016 restraints weight = 34666.436| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 27517 Z= 0.144 Angle : 0.574 16.198 37317 Z= 0.284 Chirality : 0.043 0.193 4221 Planarity : 0.003 0.039 4858 Dihedral : 5.106 39.692 3713 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % Rotamer: Outliers : 4.34 % Allowed : 19.28 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -2.34 (0.13), residues: 3423 helix: -0.71 (0.25), residues: 420 sheet: -0.18 (0.16), residues: 917 loop : -2.53 (0.12), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP E 375 HIS 0.001 0.001 HIS G 314 PHE 0.013 0.002 PHE A 281 TYR 0.017 0.001 TYR D 230 ARG 0.001 0.000 ARG A 668 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4208.03 seconds wall clock time: 79 minutes 21.21 seconds (4761.21 seconds total)