Starting phenix.real_space_refine on Thu Apr 11 17:23:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/04_2024/6klo_0713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/04_2024/6klo_0713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/04_2024/6klo_0713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/04_2024/6klo_0713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/04_2024/6klo_0713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/04_2024/6klo_0713.pdb" } resolution = 2.8 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= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 38 5.16 5 C 14584 2.51 5 N 3834 2.21 5 O 4805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 548": "OE1" <-> "OE2" Residue "A ASP 571": "OD1" <-> "OD2" Residue "A ASP 595": "OD1" <-> "OD2" Residue "A GLU 605": "OE1" <-> "OE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 368": "OD1" <-> "OD2" Residue "B TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 457": "NH1" <-> "NH2" Residue "B TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 510": "OD1" <-> "OD2" Residue "B PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 533": "OE1" <-> "OE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B GLU 585": "OE1" <-> "OE2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "C ASP 238": "OD1" <-> "OD2" Residue "C PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 262": "OE1" <-> "OE2" Residue "C ASP 317": "OD1" <-> "OD2" Residue "C GLU 372": "OE1" <-> "OE2" Residue "C TYR 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 414": "OD1" <-> "OD2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 498": "OE1" <-> "OE2" Residue "C PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 533": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 414": "OD1" <-> "OD2" Residue "D GLU 416": "OE1" <-> "OE2" Residue "D ASP 425": "OD1" <-> "OD2" Residue "D ARG 457": "NH1" <-> "NH2" Residue "D ASP 464": "OD1" <-> "OD2" Residue "D GLU 498": "OE1" <-> "OE2" Residue "D TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 533": "OE1" <-> "OE2" Residue "D ASP 571": "OD1" <-> "OD2" Residue "D ASP 581": "OD1" <-> "OD2" Residue "D GLU 585": "OE1" <-> "OE2" Residue "E PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 368": "OD1" <-> "OD2" Residue "E TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 457": "NH1" <-> "NH2" Residue "E ASP 464": "OD1" <-> "OD2" Residue "E ASP 470": "OD1" <-> "OD2" Residue "E GLU 498": "OE1" <-> "OE2" Residue "E ASP 519": "OD1" <-> "OD2" Residue "E PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 533": "OE1" <-> "OE2" Residue "E ASP 580": "OD1" <-> "OD2" Residue "E ASP 581": "OD1" <-> "OD2" Residue "E GLU 585": "OE1" <-> "OE2" Residue "E ASP 595": "OD1" <-> "OD2" Residue "F PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 368": "OD1" <-> "OD2" Residue "F ASP 414": "OD1" <-> "OD2" Residue "F ARG 457": "NH1" <-> "NH2" Residue "F TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 498": "OE1" <-> "OE2" Residue "F PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 533": "OE1" <-> "OE2" Residue "F GLU 576": "OE1" <-> "OE2" Residue "G PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 457": "NH1" <-> "NH2" Residue "G GLU 498": "OE1" <-> "OE2" Residue "G TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 519": "OD1" <-> "OD2" Residue "G PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 543": "OE1" <-> "OE2" Residue "H GLU 37": "OE1" <-> "OE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 45": "OD1" <-> "OD2" Residue "H TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 95": "OE1" <-> "OE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 117": "OE1" <-> "OE2" Residue "H ASP 134": "OD1" <-> "OD2" Residue "H ASP 148": "OD1" <-> "OD2" Residue "H TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 215": "OD1" <-> "OD2" Residue "H ASP 230": "OD1" <-> "OD2" Residue "H GLU 239": "OE1" <-> "OE2" Residue "H TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 320": "OD1" <-> "OD2" Residue "H GLU 324": "OE1" <-> "OE2" Residue "H PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 408": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 23275 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "B" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "C" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "D" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "E" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "F" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "G" Number of atoms: 2863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2863 Classifications: {'peptide': 368} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 353} Chain breaks: 1 Chain: "H" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3220 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 20, 'TRANS': 375} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.48, per 1000 atoms: 0.49 Number of scatterers: 23275 At special positions: 0 Unit cell: (146.9, 148.03, 178.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 14 19.99 S 38 16.00 O 4805 8.00 N 3834 7.00 C 14584 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: 8.67 Conformation dependent library (CDL) restraints added in 4.6 seconds 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5556 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 57 sheets defined 24.6% alpha, 35.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'A' and resid 226 through 233 Processing helix chain 'A' and resid 245 through 250 removed outlier: 4.017A pdb=" N GLU A 250 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.607A pdb=" N ILE A 428 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 470 Processing helix chain 'A' and resid 501 through 504 Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.563A pdb=" N VAL A 512 " --> pdb=" O GLN A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 555 Processing helix chain 'A' and resid 571 through 575 removed outlier: 3.808A pdb=" N VAL A 575 " --> pdb=" O GLU A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 591 Processing helix chain 'A' and resid 598 through 602 Processing helix chain 'B' and resid 226 through 233 removed outlier: 3.508A pdb=" N LYS B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 249 removed outlier: 3.793A pdb=" N ALA B 249 " --> pdb=" O ASP B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 285 through 290 Processing helix chain 'B' and resid 424 through 428 Processing helix chain 'B' and resid 462 through 470 Processing helix chain 'B' and resid 502 through 510 removed outlier: 4.677A pdb=" N SER B 507 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLN B 508 " --> pdb=" O ASN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 555 Processing helix chain 'B' and resid 580 through 591 Processing helix chain 'B' and resid 598 through 602 Processing helix chain 'C' and resid 226 through 233 Processing helix chain 'C' and resid 245 through 250 removed outlier: 4.084A pdb=" N GLU C 250 " --> pdb=" O SER C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 277 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 424 through 428 removed outlier: 3.786A pdb=" N ILE C 428 " --> pdb=" O ASP C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 Processing helix chain 'C' and resid 502 through 511 removed outlier: 4.697A pdb=" N SER C 507 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLN C 508 " --> pdb=" O ASN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 545 through 555 Processing helix chain 'C' and resid 580 through 592 removed outlier: 3.974A pdb=" N LYS C 592 " --> pdb=" O LYS C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 602 Processing helix chain 'D' and resid 226 through 233 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.795A pdb=" N ALA D 249 " --> pdb=" O ASP D 246 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU D 250 " --> pdb=" O SER D 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 246 through 250' Processing helix chain 'D' and resid 271 through 277 Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 424 through 428 removed outlier: 3.687A pdb=" N ILE D 428 " --> pdb=" O ASP D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 470 Processing helix chain 'D' and resid 502 through 510 removed outlier: 4.462A pdb=" N SER D 507 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLN D 508 " --> pdb=" O ASN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 545 through 555 Processing helix chain 'D' and resid 580 through 592 removed outlier: 3.749A pdb=" N LYS D 592 " --> pdb=" O LYS D 588 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'E' and resid 226 through 233 Processing helix chain 'E' and resid 245 through 250 removed outlier: 3.651A pdb=" N ALA E 249 " --> pdb=" O ASP E 246 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N GLU E 250 " --> pdb=" O SER E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 277 Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 424 through 428 removed outlier: 3.711A pdb=" N ILE E 428 " --> pdb=" O ASP E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 470 Processing helix chain 'E' and resid 502 through 510 removed outlier: 4.697A pdb=" N SER E 507 " --> pdb=" O SER E 503 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLN E 508 " --> pdb=" O ASN E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 545 through 554 Processing helix chain 'E' and resid 580 through 592 removed outlier: 4.113A pdb=" N LYS E 592 " --> pdb=" O LYS E 588 " (cutoff:3.500A) Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'F' and resid 226 through 233 Processing helix chain 'F' and resid 245 through 250 removed outlier: 3.521A pdb=" N PHE F 248 " --> pdb=" O ASN F 245 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA F 249 " --> pdb=" O ASP F 246 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N GLU F 250 " --> pdb=" O SER F 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 245 through 250' Processing helix chain 'F' and resid 271 through 277 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 424 through 428 removed outlier: 3.585A pdb=" N ILE F 428 " --> pdb=" O ASP F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 470 Processing helix chain 'F' and resid 502 through 512 removed outlier: 4.770A pdb=" N SER F 507 " --> pdb=" O SER F 503 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLN F 508 " --> pdb=" O ASN F 504 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL F 512 " --> pdb=" O GLN F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 554 Processing helix chain 'F' and resid 571 through 575 removed outlier: 3.826A pdb=" N VAL F 575 " --> pdb=" O GLU F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 580 through 593 removed outlier: 3.962A pdb=" N LYS F 592 " --> pdb=" O LYS F 588 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR F 593 " --> pdb=" O GLU F 589 " (cutoff:3.500A) Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'G' and resid 226 through 233 Processing helix chain 'G' and resid 245 through 249 Processing helix chain 'G' and resid 271 through 277 Processing helix chain 'G' and resid 285 through 290 Processing helix chain 'G' and resid 424 through 428 removed outlier: 3.543A pdb=" N ILE G 428 " --> pdb=" O ASP G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 470 Processing helix chain 'G' and resid 502 through 510 removed outlier: 4.590A pdb=" N SER G 507 " --> pdb=" O SER G 503 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N GLN G 508 " --> pdb=" O ASN G 504 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 555 Processing helix chain 'G' and resid 571 through 575 removed outlier: 3.920A pdb=" N VAL G 575 " --> pdb=" O GLU G 572 " (cutoff:3.500A) Processing helix chain 'G' and resid 580 through 593 removed outlier: 4.068A pdb=" N TYR G 593 " --> pdb=" O GLU G 589 " (cutoff:3.500A) Processing helix chain 'G' and resid 598 through 602 Processing helix chain 'H' and resid 19 through 28 Processing helix chain 'H' and resid 32 through 56 removed outlier: 4.079A pdb=" N LYS H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLU H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLN H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 59 No H-bonds generated for 'chain 'H' and resid 57 through 59' Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 69 through 81 Processing helix chain 'H' and resid 96 through 101 Processing helix chain 'H' and resid 115 through 126 Processing helix chain 'H' and resid 216 through 228 removed outlier: 3.662A pdb=" N GLY H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 231 through 235 Processing helix chain 'H' and resid 236 through 248 Processing helix chain 'H' and resid 249 through 259 removed outlier: 4.392A pdb=" N ALA H 253 " --> pdb=" O GLY H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 266 Processing helix chain 'H' and resid 268 through 281 Processing helix chain 'H' and resid 298 through 302 removed outlier: 3.971A pdb=" N GLU H 301 " --> pdb=" O GLY H 298 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 312 removed outlier: 3.510A pdb=" N TYR H 311 " --> pdb=" O SER H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 368 through 372 removed outlier: 3.813A pdb=" N ILE H 372 " --> pdb=" O LEU H 369 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 310 removed outlier: 6.757A pdb=" N ASN A 391 " --> pdb=" O GLU A 304 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU A 306 " --> pdb=" O ASN A 389 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ASN A 389 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ILE A 308 " --> pdb=" O TYR A 387 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TYR A 387 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 438 removed outlier: 4.584A pdb=" N ILE A 459 " --> pdb=" O ILE A 388 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 325 removed outlier: 3.662A pdb=" N SER A 323 " --> pdb=" O SER A 369 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 369 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA A 325 " --> pdb=" O GLN A 367 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR G 326 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS G 320 " --> pdb=" O TRP A 374 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR F 321 " --> pdb=" O GLY F 371 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER F 323 " --> pdb=" O SER F 369 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER F 369 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER E 369 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 326 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN E 370 " --> pdb=" O ARG D 324 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR D 321 " --> pdb=" O GLY D 371 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA D 325 " --> pdb=" O GLN D 367 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASP D 368 " --> pdb=" O THR C 326 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN D 370 " --> pdb=" O ARG C 324 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG C 324 " --> pdb=" O ASN D 370 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N SER C 369 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 322 " --> pdb=" O GLU C 372 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER B 323 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN B 370 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG A 324 " --> pdb=" O ASN B 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 416 through 422 removed outlier: 6.784A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TYR A 403 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASN A 431 " --> pdb=" O TYR A 403 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 416 through 422 removed outlier: 6.784A pdb=" N LEU A 411 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR A 420 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N THR A 409 " --> pdb=" O THR A 420 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS A 422 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N VAL A 405 " --> pdb=" O SER A 483 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A 483 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N GLN A 481 " --> pdb=" O PRO A 407 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR A 409 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 479 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LEU A 411 " --> pdb=" O LEU A 477 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LEU A 477 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 413 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE A 475 " --> pdb=" O LEU A 413 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 488 through 489 Processing sheet with id=AA8, first strand: chain 'A' and resid 524 through 530 removed outlier: 9.140A pdb=" N ILE A 610 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER A 515 " --> pdb=" O ILE A 610 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE A 612 " --> pdb=" O SER A 515 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE A 517 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 557 through 559 Processing sheet with id=AB1, first strand: chain 'B' and resid 234 through 237 Processing sheet with id=AB2, first strand: chain 'B' and resid 299 through 310 removed outlier: 6.783A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B 306 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN B 389 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 308 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B 387 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 299 through 310 removed outlier: 6.783A pdb=" N ASN B 391 " --> pdb=" O GLU B 304 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU B 306 " --> pdb=" O ASN B 389 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASN B 389 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ILE B 308 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B 387 " --> pdb=" O ILE B 308 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ILE B 459 " --> pdb=" O ILE B 388 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 416 through 422 removed outlier: 3.559A pdb=" N GLU B 416 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR B 403 " --> pdb=" O ASN B 431 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B 431 " --> pdb=" O TYR B 403 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 416 through 422 removed outlier: 3.559A pdb=" N GLU B 416 " --> pdb=" O LEU B 413 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 411 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR B 420 " --> pdb=" O THR B 409 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N THR B 409 " --> pdb=" O THR B 420 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS B 422 " --> pdb=" O PRO B 407 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS B 404 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY B 484 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR B 406 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N VAL B 482 " --> pdb=" O THR B 406 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR B 408 " --> pdb=" O THR B 480 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 488 through 489 Processing sheet with id=AB7, first strand: chain 'B' and resid 524 through 530 removed outlier: 9.183A pdb=" N ILE B 610 " --> pdb=" O SER B 513 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER B 515 " --> pdb=" O ILE B 610 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE B 612 " --> pdb=" O SER B 515 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE B 517 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 557 through 559 removed outlier: 3.694A pdb=" N LEU B 562 " --> pdb=" O ASN B 559 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 234 through 237 Processing sheet with id=AC1, first strand: chain 'C' and resid 299 through 310 removed outlier: 6.727A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU C 306 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN C 389 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE C 308 " --> pdb=" O TYR C 387 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR C 387 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 299 through 310 removed outlier: 6.727A pdb=" N ASN C 391 " --> pdb=" O GLU C 304 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU C 306 " --> pdb=" O ASN C 389 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN C 389 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE C 308 " --> pdb=" O TYR C 387 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N TYR C 387 " --> pdb=" O ILE C 308 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE C 459 " --> pdb=" O ILE C 388 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 416 through 422 removed outlier: 6.829A pdb=" N LEU C 411 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR C 420 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N THR C 409 " --> pdb=" O THR C 420 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS C 422 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL C 405 " --> pdb=" O SER C 483 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER C 483 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLN C 481 " --> pdb=" O PRO C 407 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N THR C 409 " --> pdb=" O THR C 479 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR C 479 " --> pdb=" O THR C 409 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU C 411 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU C 477 " --> pdb=" O LEU C 411 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 488 through 489 Processing sheet with id=AC5, first strand: chain 'C' and resid 524 through 530 Processing sheet with id=AC6, first strand: chain 'C' and resid 557 through 559 removed outlier: 3.603A pdb=" N LEU C 562 " --> pdb=" O ASN C 559 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 234 through 237 Processing sheet with id=AC8, first strand: chain 'D' and resid 299 through 310 removed outlier: 6.806A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 299 through 310 removed outlier: 6.806A pdb=" N ASN D 391 " --> pdb=" O GLU D 304 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU D 306 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASN D 389 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ILE D 308 " --> pdb=" O TYR D 387 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TYR D 387 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE D 459 " --> pdb=" O ILE D 388 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 416 through 422 removed outlier: 6.775A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR D 403 " --> pdb=" O ASN D 431 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASN D 431 " --> pdb=" O TYR D 403 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 416 through 422 removed outlier: 6.775A pdb=" N LEU D 411 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR D 420 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N THR D 409 " --> pdb=" O THR D 420 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS D 422 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL D 405 " --> pdb=" O SER D 483 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N SER D 483 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLN D 481 " --> pdb=" O PRO D 407 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR D 409 " --> pdb=" O THR D 479 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR D 479 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N LEU D 411 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N LEU D 477 " --> pdb=" O LEU D 411 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 488 through 489 Processing sheet with id=AD4, first strand: chain 'D' and resid 524 through 530 removed outlier: 9.155A pdb=" N ILE D 610 " --> pdb=" O SER D 513 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N SER D 515 " --> pdb=" O ILE D 610 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ILE D 612 " --> pdb=" O SER D 515 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE D 517 " --> pdb=" O ILE D 612 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 557 through 559 Processing sheet with id=AD6, first strand: chain 'E' and resid 234 through 236 Processing sheet with id=AD7, first strand: chain 'E' and resid 299 through 310 removed outlier: 6.763A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE E 308 " --> pdb=" O TYR E 387 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR E 387 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 299 through 310 removed outlier: 6.763A pdb=" N ASN E 391 " --> pdb=" O GLU E 304 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU E 306 " --> pdb=" O ASN E 389 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ASN E 389 " --> pdb=" O LEU E 306 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE E 308 " --> pdb=" O TYR E 387 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N TYR E 387 " --> pdb=" O ILE E 308 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ILE E 459 " --> pdb=" O ILE E 388 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 416 through 422 removed outlier: 5.422A pdb=" N THR E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU E 413 " --> pdb=" O THR E 417 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 419 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N TYR E 403 " --> pdb=" O ASN E 431 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN E 431 " --> pdb=" O TYR E 403 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 416 through 422 removed outlier: 5.422A pdb=" N THR E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU E 413 " --> pdb=" O THR E 417 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 419 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS E 404 " --> pdb=" O GLY E 484 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLY E 484 " --> pdb=" O LYS E 404 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR E 406 " --> pdb=" O VAL E 482 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL E 482 " --> pdb=" O THR E 406 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N THR E 408 " --> pdb=" O THR E 480 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 524 through 530 removed outlier: 9.196A pdb=" N ILE E 610 " --> pdb=" O SER E 513 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N SER E 515 " --> pdb=" O ILE E 610 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ILE E 612 " --> pdb=" O SER E 515 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ILE E 517 " --> pdb=" O ILE E 612 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 557 through 559 Processing sheet with id=AE4, first strand: chain 'F' and resid 234 through 237 Processing sheet with id=AE5, first strand: chain 'F' and resid 299 through 310 removed outlier: 6.766A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU F 306 " --> pdb=" O ASN F 389 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN F 389 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE F 308 " --> pdb=" O TYR F 387 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR F 387 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 299 through 310 removed outlier: 6.766A pdb=" N ASN F 391 " --> pdb=" O GLU F 304 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU F 306 " --> pdb=" O ASN F 389 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASN F 389 " --> pdb=" O LEU F 306 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE F 308 " --> pdb=" O TYR F 387 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TYR F 387 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE F 459 " --> pdb=" O ILE F 388 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 416 through 422 removed outlier: 6.736A pdb=" N LEU F 411 " --> pdb=" O LEU F 418 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N THR F 420 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR F 409 " --> pdb=" O THR F 420 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N LYS F 422 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N VAL F 405 " --> pdb=" O SER F 483 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N SER F 483 " --> pdb=" O VAL F 405 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N GLN F 481 " --> pdb=" O PRO F 407 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR F 409 " --> pdb=" O THR F 479 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR F 479 " --> pdb=" O THR F 409 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N LEU F 411 " --> pdb=" O LEU F 477 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU F 477 " --> pdb=" O LEU F 411 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 524 through 530 Processing sheet with id=AE9, first strand: chain 'F' and resid 557 through 559 removed outlier: 3.901A pdb=" N LEU F 562 " --> pdb=" O ASN F 559 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 234 through 237 Processing sheet with id=AF2, first strand: chain 'G' and resid 299 through 301 removed outlier: 3.650A pdb=" N GLU G 436 " --> pdb=" O ASN G 396 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 305 through 310 removed outlier: 3.718A pdb=" N ASN G 305 " --> pdb=" O ASN G 391 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE G 459 " --> pdb=" O ILE G 388 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 417 through 422 removed outlier: 6.815A pdb=" N LEU G 411 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR G 420 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR G 409 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS G 422 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TYR G 403 " --> pdb=" O ASN G 431 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN G 431 " --> pdb=" O TYR G 403 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 417 through 422 removed outlier: 6.815A pdb=" N LEU G 411 " --> pdb=" O LEU G 418 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR G 420 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N THR G 409 " --> pdb=" O THR G 420 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS G 422 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL G 405 " --> pdb=" O SER G 483 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N SER G 483 " --> pdb=" O VAL G 405 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN G 481 " --> pdb=" O PRO G 407 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR G 409 " --> pdb=" O THR G 479 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR G 479 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N LEU G 411 " --> pdb=" O LEU G 477 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N LEU G 477 " --> pdb=" O LEU G 411 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'G' and resid 488 through 489 Processing sheet with id=AF7, first strand: chain 'G' and resid 524 through 530 removed outlier: 9.050A pdb=" N ILE G 610 " --> pdb=" O SER G 513 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER G 515 " --> pdb=" O ILE G 610 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE G 612 " --> pdb=" O SER G 515 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE G 517 " --> pdb=" O ILE G 612 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 557 through 559 Processing sheet with id=AF9, first strand: chain 'H' and resid 89 through 95 removed outlier: 3.976A pdb=" N LEU H 154 " --> pdb=" O GLU H 95 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS H 159 " --> pdb=" O ALA H 205 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ILE H 207 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS H 198 " --> pdb=" O VAL H 194 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL H 194 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N TYR H 200 " --> pdb=" O ARG H 192 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ARG H 192 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LYS H 202 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE H 190 " --> pdb=" O LYS H 202 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU H 204 " --> pdb=" O ASP H 188 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER H 184 " --> pdb=" O VAL H 208 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 136 through 139 Processing sheet with id=AG2, first strand: chain 'H' and resid 291 through 297 removed outlier: 3.565A pdb=" N ILE H 354 " --> pdb=" O SER H 297 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE H 355 " --> pdb=" O LEU H 407 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ALA H 409 " --> pdb=" O ILE H 355 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ARG H 357 " --> pdb=" O ALA H 409 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU H 411 " --> pdb=" O ARG H 357 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ASN H 359 " --> pdb=" O LEU H 411 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N THR H 410 " --> pdb=" O ILE H 391 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE H 391 " --> pdb=" O THR H 410 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 339 through 340 866 hydrogen bonds defined for protein. 2217 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: 8.77 Time building geometry restraints manager: 9.50 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: 7627 1.34 - 1.45: 3155 1.45 - 1.57: 12805 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 23656 Sorted by residual: bond pdb=" CA ALA C 288 " pdb=" C ALA C 288 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.80e-02 3.09e+03 3.75e+00 bond pdb=" CA HIS B 313 " pdb=" CB HIS B 313 " ideal model delta sigma weight residual 1.526 1.499 0.028 1.53e-02 4.27e+03 3.24e+00 bond pdb=" CG PRO A 439 " pdb=" CD PRO A 439 " ideal model delta sigma weight residual 1.512 1.469 0.043 2.70e-02 1.37e+03 2.51e+00 bond pdb=" CG PRO E 439 " pdb=" CD PRO E 439 " ideal model delta sigma weight residual 1.512 1.470 0.042 2.70e-02 1.37e+03 2.40e+00 bond pdb=" CG PRO F 439 " pdb=" CD PRO F 439 " ideal model delta sigma weight residual 1.512 1.470 0.042 2.70e-02 1.37e+03 2.37e+00 ... (remaining 23651 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.89: 543 106.89 - 113.67: 13217 113.67 - 120.46: 8616 120.46 - 127.25: 9532 127.25 - 134.04: 148 Bond angle restraints: 32056 Sorted by residual: angle pdb=" N VAL B 602 " pdb=" CA VAL B 602 " pdb=" C VAL B 602 " ideal model delta sigma weight residual 110.21 106.58 3.63 1.13e+00 7.83e-01 1.03e+01 angle pdb=" C SER B 247 " pdb=" N PHE B 248 " pdb=" CA PHE B 248 " ideal model delta sigma weight residual 123.25 118.02 5.23 1.69e+00 3.50e-01 9.58e+00 angle pdb=" N VAL G 602 " pdb=" CA VAL G 602 " pdb=" C VAL G 602 " ideal model delta sigma weight residual 110.05 106.73 3.32 1.09e+00 8.42e-01 9.25e+00 angle pdb=" CA LEU A 604 " pdb=" C LEU A 604 " pdb=" N GLU A 605 " ideal model delta sigma weight residual 114.17 118.17 -4.00 1.45e+00 4.76e-01 7.62e+00 angle pdb=" CA ALA C 288 " pdb=" C ALA C 288 " pdb=" N ARG C 289 " ideal model delta sigma weight residual 118.27 122.51 -4.24 1.59e+00 3.96e-01 7.13e+00 ... (remaining 32051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.95: 13159 16.95 - 33.90: 1029 33.90 - 50.85: 170 50.85 - 67.80: 43 67.80 - 84.75: 19 Dihedral angle restraints: 14420 sinusoidal: 5744 harmonic: 8676 Sorted by residual: dihedral pdb=" CA GLU G 605 " pdb=" C GLU G 605 " pdb=" N ARG G 606 " pdb=" CA ARG G 606 " ideal model delta harmonic sigma weight residual 180.00 147.74 32.26 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA VAL A 602 " pdb=" C VAL A 602 " pdb=" N LYS A 603 " pdb=" CA LYS A 603 " ideal model delta harmonic sigma weight residual 180.00 -152.33 -27.67 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA VAL F 602 " pdb=" C VAL F 602 " pdb=" N LYS F 603 " pdb=" CA LYS F 603 " ideal model delta harmonic sigma weight residual -180.00 -153.60 -26.40 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 14417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2194 0.036 - 0.073: 908 0.073 - 0.109: 343 0.109 - 0.145: 143 0.145 - 0.181: 7 Chirality restraints: 3595 Sorted by residual: chirality pdb=" CB THR A 406 " pdb=" CA THR A 406 " pdb=" OG1 THR A 406 " pdb=" CG2 THR A 406 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.22e-01 chirality pdb=" CA ASN E 224 " pdb=" N ASN E 224 " pdb=" C ASN E 224 " pdb=" CB ASN E 224 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.18e-01 chirality pdb=" CA ASN F 224 " pdb=" N ASN F 224 " pdb=" C ASN F 224 " pdb=" CB ASN F 224 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 3592 not shown) Planarity restraints: 4197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 268 " -0.037 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO C 269 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR F 438 " 0.035 5.00e-02 4.00e+02 5.27e-02 4.45e+00 pdb=" N PRO F 439 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 439 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 439 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 268 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO G 269 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO G 269 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO G 269 " 0.028 5.00e-02 4.00e+02 ... (remaining 4194 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1552 2.73 - 3.27: 22562 3.27 - 3.81: 37179 3.81 - 4.36: 48743 4.36 - 4.90: 82670 Nonbonded interactions: 192706 Sorted by model distance: nonbonded pdb=" OE1 GLU B 230 " pdb=" OG SER B 258 " model vdw 2.185 2.440 nonbonded pdb=" O ILE D 509 " pdb=" OG SER D 513 " model vdw 2.231 2.440 nonbonded pdb=" OD1 ASP C 221 " pdb="CA CA C1002 " model vdw 2.242 2.510 nonbonded pdb=" OE1 GLU C 230 " pdb=" OG SER C 258 " model vdw 2.246 2.440 nonbonded pdb=" O ILE E 225 " pdb="CA CA E1002 " model vdw 2.249 2.510 ... (remaining 192701 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.130 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: 0.030 Extract box with map and model: 8.070 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 60.840 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.005 0.050 23656 Z= 0.304 Angle : 0.600 6.886 32056 Z= 0.348 Chirality : 0.048 0.181 3595 Planarity : 0.005 0.055 4197 Dihedral : 13.062 84.749 8864 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.12 % Allowed : 2.93 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.13), residues: 2942 helix: -2.44 (0.17), residues: 554 sheet: -1.54 (0.17), residues: 792 loop : -2.23 (0.13), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 223 HIS 0.002 0.001 HIS H 157 PHE 0.016 0.002 PHE A 248 TYR 0.017 0.001 TYR F 438 ARG 0.006 0.000 ARG D 606 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 360 time to evaluate : 2.645 Fit side-chains REVERT: B 311 ASN cc_start: 0.8730 (p0) cc_final: 0.8412 (p0) REVERT: C 372 GLU cc_start: 0.7392 (mt-10) cc_final: 0.7175 (mt-10) REVERT: C 489 LYS cc_start: 0.7819 (mttp) cc_final: 0.7545 (mttt) REVERT: D 463 TYR cc_start: 0.8628 (t80) cc_final: 0.8397 (t80) REVERT: F 414 ASP cc_start: 0.7778 (t0) cc_final: 0.7563 (t0) REVERT: H 44 LYS cc_start: 0.6841 (ptpp) cc_final: 0.6610 (pptt) REVERT: H 56 ARG cc_start: 0.8367 (ttp80) cc_final: 0.7891 (ppt-90) REVERT: H 63 GLN cc_start: 0.6564 (mt0) cc_final: 0.6349 (mt0) REVERT: H 182 ASP cc_start: 0.8320 (t70) cc_final: 0.8105 (t0) REVERT: H 347 SER cc_start: 0.6503 (m) cc_final: 0.6278 (m) outliers start: 3 outliers final: 2 residues processed: 363 average time/residue: 1.5412 time to fit residues: 632.3743 Evaluate side-chains 216 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 214 time to evaluate : 3.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain H residue 233 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 245 optimal weight: 0.0970 chunk 220 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 264 optimal weight: 0.2980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 435 ASN B 305 ASN B 391 ASN B 492 GLN B 582 ASN C 318 GLN D 590 GLN E 245 ASN E 582 ASN F 494 GLN G 449 ASN G 534 GLN G 559 ASN H 199 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23656 Z= 0.196 Angle : 0.520 7.232 32056 Z= 0.287 Chirality : 0.046 0.152 3595 Planarity : 0.004 0.048 4197 Dihedral : 5.199 29.316 3184 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.43 % Allowed : 10.41 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % 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: -2.07 (0.14), residues: 2942 helix: -1.01 (0.20), residues: 568 sheet: -0.64 (0.17), residues: 764 loop : -1.90 (0.14), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 374 HIS 0.005 0.001 HIS H 157 PHE 0.025 0.001 PHE C 248 TYR 0.014 0.001 TYR F 438 ARG 0.005 0.000 ARG F 528 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 234 time to evaluate : 2.927 Fit side-chains REVERT: A 441 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8166 (ttpp) REVERT: B 311 ASN cc_start: 0.8742 (p0) cc_final: 0.8405 (p0) REVERT: B 384 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7932 (mt-10) REVERT: C 296 TYR cc_start: 0.8828 (t80) cc_final: 0.8509 (t80) REVERT: C 489 LYS cc_start: 0.7801 (mttp) cc_final: 0.7554 (mttt) REVERT: D 463 TYR cc_start: 0.8592 (t80) cc_final: 0.8380 (t80) REVERT: E 620 ASN cc_start: 0.4281 (OUTLIER) cc_final: 0.3490 (p0) REVERT: F 498 GLU cc_start: 0.6698 (tp30) cc_final: 0.6493 (tm-30) REVERT: G 317 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7574 (p0) REVERT: H 143 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7540 (mt-10) REVERT: H 180 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7953 (tt0) REVERT: H 219 LYS cc_start: 0.7058 (tptt) cc_final: 0.6852 (tptp) REVERT: H 339 THR cc_start: 0.7794 (p) cc_final: 0.7516 (t) REVERT: H 347 SER cc_start: 0.6692 (m) cc_final: 0.6021 (t) outliers start: 37 outliers final: 16 residues processed: 260 average time/residue: 1.5099 time to fit residues: 446.2599 Evaluate side-chains 231 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 210 time to evaluate : 2.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain B residue 305 ASN Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 620 ASN Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain H residue 76 LEU Chi-restraints excluded: chain H residue 180 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 72 optimal weight: 0.0670 chunk 264 optimal weight: 8.9990 chunk 285 optimal weight: 8.9990 chunk 235 optimal weight: 0.9980 chunk 262 optimal weight: 5.9990 chunk 90 optimal weight: 0.0270 chunk 212 optimal weight: 0.6980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN B 264 ASN B 582 ASN C 318 GLN E 582 ASN F 494 GLN G 534 GLN H 233 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23656 Z= 0.149 Angle : 0.481 6.987 32056 Z= 0.265 Chirality : 0.044 0.138 3595 Planarity : 0.004 0.046 4197 Dihedral : 4.869 27.454 3182 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.85 % Allowed : 11.87 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.49 (0.14), residues: 2942 helix: -0.34 (0.22), residues: 570 sheet: -0.13 (0.18), residues: 764 loop : -1.70 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 374 HIS 0.003 0.001 HIS H 157 PHE 0.022 0.001 PHE C 248 TYR 0.012 0.001 TYR F 438 ARG 0.003 0.000 ARG F 528 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 245 time to evaluate : 2.821 Fit side-chains revert: symmetry clash REVERT: A 562 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7528 (tp) REVERT: B 281 ASP cc_start: 0.8304 (t0) cc_final: 0.7979 (t0) REVERT: B 289 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7555 (ptp-170) REVERT: B 311 ASN cc_start: 0.8693 (p0) cc_final: 0.8350 (p0) REVERT: B 533 GLU cc_start: 0.8091 (tt0) cc_final: 0.7836 (tt0) REVERT: C 296 TYR cc_start: 0.8741 (t80) cc_final: 0.8409 (t80) REVERT: C 489 LYS cc_start: 0.7621 (mttp) cc_final: 0.7372 (mttt) REVERT: D 463 TYR cc_start: 0.8568 (t80) cc_final: 0.8354 (t80) REVERT: E 620 ASN cc_start: 0.4254 (OUTLIER) cc_final: 0.3456 (p0) REVERT: G 317 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7461 (p0) REVERT: G 489 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7375 (mttp) REVERT: G 532 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7886 (ptmm) REVERT: H 143 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7532 (mt-10) REVERT: H 180 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7898 (tp30) REVERT: H 219 LYS cc_start: 0.7013 (tptt) cc_final: 0.6813 (tptp) REVERT: H 234 LYS cc_start: 0.7363 (tmmt) cc_final: 0.7102 (ptmt) REVERT: H 339 THR cc_start: 0.7832 (p) cc_final: 0.7591 (t) REVERT: H 347 SER cc_start: 0.6813 (m) cc_final: 0.6173 (t) outliers start: 48 outliers final: 18 residues processed: 276 average time/residue: 1.4971 time to fit residues: 470.5678 Evaluate side-chains 246 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 221 time to evaluate : 2.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 562 LEU Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 620 ASN Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 589 GLU Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 532 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 233 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 126 optimal weight: 0.0770 chunk 177 optimal weight: 0.6980 chunk 265 optimal weight: 0.7980 chunk 281 optimal weight: 10.0000 chunk 138 optimal weight: 0.8980 chunk 251 optimal weight: 2.9990 chunk 75 optimal weight: 0.0770 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN C 318 GLN E 582 ASN F 494 GLN G 534 GLN H 199 GLN H 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 23656 Z= 0.140 Angle : 0.468 7.710 32056 Z= 0.257 Chirality : 0.044 0.137 3595 Planarity : 0.004 0.048 4197 Dihedral : 4.682 26.265 3182 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.62 % Allowed : 13.45 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.14), residues: 2942 helix: -0.05 (0.22), residues: 578 sheet: 0.30 (0.18), residues: 757 loop : -1.62 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 374 HIS 0.002 0.000 HIS H 157 PHE 0.019 0.001 PHE B 248 TYR 0.014 0.001 TYR F 296 ARG 0.003 0.000 ARG F 528 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 235 time to evaluate : 2.846 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 289 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7775 (ptp-170) REVERT: B 311 ASN cc_start: 0.8555 (p0) cc_final: 0.8277 (p0) REVERT: B 533 GLU cc_start: 0.8112 (tt0) cc_final: 0.7862 (tt0) REVERT: B 589 GLU cc_start: 0.8066 (pp20) cc_final: 0.7378 (tm-30) REVERT: C 489 LYS cc_start: 0.7573 (mttp) cc_final: 0.7336 (mttt) REVERT: D 463 TYR cc_start: 0.8552 (t80) cc_final: 0.8350 (t80) REVERT: E 620 ASN cc_start: 0.4246 (OUTLIER) cc_final: 0.3437 (p0) REVERT: F 320 LYS cc_start: 0.7604 (tttt) cc_final: 0.7367 (tttt) REVERT: F 562 LEU cc_start: 0.7559 (pt) cc_final: 0.6965 (mt) REVERT: G 384 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7287 (tp30) REVERT: G 489 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7443 (mttm) REVERT: H 180 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7802 (tp30) REVERT: H 234 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7043 (pttt) REVERT: H 339 THR cc_start: 0.7827 (p) cc_final: 0.7590 (t) REVERT: H 347 SER cc_start: 0.7008 (m) cc_final: 0.6342 (t) outliers start: 42 outliers final: 18 residues processed: 264 average time/residue: 1.5128 time to fit residues: 453.7183 Evaluate side-chains 237 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 213 time to evaluate : 2.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 620 ASN Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 589 GLU Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 285 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 240 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN B 582 ASN D 251 GLN D 559 ASN E 582 ASN F 494 GLN G 534 GLN H 199 GLN H 233 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 23656 Z= 0.366 Angle : 0.563 7.811 32056 Z= 0.307 Chirality : 0.048 0.160 3595 Planarity : 0.005 0.050 4197 Dihedral : 5.198 29.463 3182 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.16 % Allowed : 13.96 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.14), residues: 2942 helix: -0.04 (0.22), residues: 571 sheet: 0.35 (0.18), residues: 757 loop : -1.58 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 374 HIS 0.002 0.001 HIS H 157 PHE 0.027 0.002 PHE C 248 TYR 0.023 0.002 TYR F 296 ARG 0.004 0.000 ARG E 393 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 213 time to evaluate : 2.610 Fit side-chains revert: symmetry clash REVERT: A 441 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8115 (ttpp) REVERT: B 281 ASP cc_start: 0.8282 (t0) cc_final: 0.7944 (t0) REVERT: B 289 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7690 (ptp-170) REVERT: B 311 ASN cc_start: 0.8668 (p0) cc_final: 0.8405 (p0) REVERT: B 589 GLU cc_start: 0.8085 (pp20) cc_final: 0.7498 (tm-30) REVERT: C 489 LYS cc_start: 0.7777 (mttp) cc_final: 0.7453 (mttt) REVERT: D 463 TYR cc_start: 0.8635 (t80) cc_final: 0.8431 (t80) REVERT: E 620 ASN cc_start: 0.4101 (OUTLIER) cc_final: 0.3255 (p0) REVERT: G 317 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7556 (p0) REVERT: G 384 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: G 489 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7789 (mttt) REVERT: H 180 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7810 (tp30) REVERT: H 234 LYS cc_start: 0.7438 (OUTLIER) cc_final: 0.6975 (ptmm) REVERT: H 339 THR cc_start: 0.7837 (p) cc_final: 0.7609 (t) outliers start: 56 outliers final: 33 residues processed: 252 average time/residue: 1.4671 time to fit residues: 421.5276 Evaluate side-chains 237 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 196 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 557 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 315 SER Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 532 LYS Chi-restraints excluded: chain B residue 619 THR Chi-restraints excluded: chain C residue 279 SER Chi-restraints excluded: chain C residue 310 THR Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain E residue 315 SER Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 590 GLN Chi-restraints excluded: chain E residue 620 ASN Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 589 GLU Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain G residue 598 LYS Chi-restraints excluded: chain G residue 620 ASN Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 285 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 2.9990 chunk 253 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 281 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 23 optimal weight: 0.0970 chunk 93 optimal weight: 0.0040 chunk 147 optimal weight: 0.0670 overall best weight: 0.3128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 305 ASN B 391 ASN B 582 ASN C 318 GLN D 251 GLN ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 ASN F 222 ASN F 494 GLN F 508 GLN G 534 GLN H 48 GLN H 199 GLN H 233 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23656 Z= 0.125 Angle : 0.468 8.243 32056 Z= 0.256 Chirality : 0.044 0.154 3595 Planarity : 0.004 0.049 4197 Dihedral : 4.590 26.221 3180 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.39 % Allowed : 15.34 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 2942 helix: 0.13 (0.22), residues: 578 sheet: 0.67 (0.18), residues: 757 loop : -1.53 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 374 HIS 0.002 0.000 HIS H 157 PHE 0.017 0.001 PHE B 248 TYR 0.014 0.001 TYR H 251 ARG 0.005 0.000 ARG G 457 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 234 time to evaluate : 2.889 Fit side-chains revert: symmetry clash REVERT: A 395 TYR cc_start: 0.8484 (m-80) cc_final: 0.8209 (m-80) REVERT: B 289 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.7635 (ptp-170) REVERT: B 311 ASN cc_start: 0.8485 (p0) cc_final: 0.8240 (p0) REVERT: B 589 GLU cc_start: 0.8018 (pp20) cc_final: 0.7390 (tm-30) REVERT: C 489 LYS cc_start: 0.7525 (mttp) cc_final: 0.7259 (mttt) REVERT: D 318 GLN cc_start: 0.7570 (mt0) cc_final: 0.7342 (mt0) REVERT: D 463 TYR cc_start: 0.8530 (t80) cc_final: 0.8325 (t80) REVERT: E 620 ASN cc_start: 0.4169 (OUTLIER) cc_final: 0.3370 (p0) REVERT: F 562 LEU cc_start: 0.7632 (pt) cc_final: 0.6972 (mt) REVERT: F 564 TYR cc_start: 0.7986 (m-10) cc_final: 0.7731 (m-80) REVERT: G 446 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.7969 (mt) REVERT: G 564 TYR cc_start: 0.7738 (m-80) cc_final: 0.7311 (m-80) REVERT: H 234 LYS cc_start: 0.7339 (OUTLIER) cc_final: 0.6987 (ptmm) outliers start: 36 outliers final: 15 residues processed: 256 average time/residue: 1.4239 time to fit residues: 417.6309 Evaluate side-chains 223 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 620 ASN Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 589 GLU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain H residue 233 ASN Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 347 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 0.7980 chunk 31 optimal weight: 0.0970 chunk 160 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 chunk 237 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 280 optimal weight: 0.7980 chunk 175 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN B 582 ASN C 318 GLN D 251 GLN D 370 ASN ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 ASN F 222 ASN F 494 GLN G 534 GLN H 48 GLN H 233 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 23656 Z= 0.154 Angle : 0.472 8.186 32056 Z= 0.258 Chirality : 0.044 0.144 3595 Planarity : 0.004 0.047 4197 Dihedral : 4.551 26.068 3180 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.58 % Allowed : 15.73 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.15), residues: 2942 helix: 0.21 (0.22), residues: 578 sheet: 0.83 (0.18), residues: 757 loop : -1.48 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 374 HIS 0.001 0.000 HIS H 157 PHE 0.018 0.001 PHE B 248 TYR 0.019 0.001 TYR F 296 ARG 0.004 0.000 ARG G 457 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 214 time to evaluate : 2.716 Fit side-chains revert: symmetry clash REVERT: A 395 TYR cc_start: 0.8508 (m-80) cc_final: 0.8177 (m-80) REVERT: B 289 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7703 (ptp-170) REVERT: B 311 ASN cc_start: 0.8548 (p0) cc_final: 0.8282 (p0) REVERT: C 489 LYS cc_start: 0.7534 (mttp) cc_final: 0.7274 (mttt) REVERT: D 318 GLN cc_start: 0.7538 (mt0) cc_final: 0.7309 (mt0) REVERT: D 463 TYR cc_start: 0.8546 (t80) cc_final: 0.8346 (t80) REVERT: E 620 ASN cc_start: 0.4263 (OUTLIER) cc_final: 0.3412 (p0) REVERT: F 562 LEU cc_start: 0.7559 (pt) cc_final: 0.6956 (mt) REVERT: F 564 TYR cc_start: 0.7947 (m-10) cc_final: 0.7738 (m-80) REVERT: G 281 ASP cc_start: 0.8385 (t0) cc_final: 0.8162 (t0) REVERT: G 317 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7256 (p0) REVERT: G 384 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7179 (tt0) REVERT: G 446 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8076 (mt) REVERT: H 180 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7894 (tp30) REVERT: H 234 LYS cc_start: 0.7323 (OUTLIER) cc_final: 0.7037 (ptmt) REVERT: H 258 LEU cc_start: 0.5600 (OUTLIER) cc_final: 0.5370 (mm) outliers start: 41 outliers final: 21 residues processed: 238 average time/residue: 1.4827 time to fit residues: 402.5953 Evaluate side-chains 234 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 205 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 441 LYS Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 620 ASN Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 589 GLU Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 233 ASN Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 285 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 0.7980 chunk 112 optimal weight: 0.0270 chunk 167 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 191 optimal weight: 0.0030 chunk 138 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 220 optimal weight: 4.9990 overall best weight: 0.5048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 ASN B 391 ASN B 582 ASN C 318 GLN D 251 GLN D 370 ASN E 582 ASN F 494 GLN G 534 GLN H 48 GLN H 199 GLN H 233 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23656 Z= 0.140 Angle : 0.474 8.391 32056 Z= 0.257 Chirality : 0.044 0.151 3595 Planarity : 0.004 0.048 4197 Dihedral : 4.488 25.772 3180 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.39 % Allowed : 16.08 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.15), residues: 2942 helix: 0.25 (0.22), residues: 578 sheet: 0.93 (0.18), residues: 757 loop : -1.43 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 374 HIS 0.001 0.000 HIS H 157 PHE 0.017 0.001 PHE B 248 TYR 0.019 0.001 TYR F 296 ARG 0.004 0.000 ARG G 457 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 219 time to evaluate : 2.758 Fit side-chains revert: symmetry clash REVERT: A 395 TYR cc_start: 0.8473 (m-80) cc_final: 0.8190 (m-80) REVERT: B 289 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.7784 (mtm180) REVERT: B 311 ASN cc_start: 0.8511 (p0) cc_final: 0.8224 (p0) REVERT: D 318 GLN cc_start: 0.7564 (mt0) cc_final: 0.7349 (mt0) REVERT: D 463 TYR cc_start: 0.8544 (t80) cc_final: 0.8344 (t80) REVERT: E 620 ASN cc_start: 0.4258 (OUTLIER) cc_final: 0.3420 (p0) REVERT: F 451 MET cc_start: 0.8493 (ptm) cc_final: 0.8264 (ptt) REVERT: F 562 LEU cc_start: 0.7561 (pt) cc_final: 0.6956 (mt) REVERT: G 281 ASP cc_start: 0.8365 (t0) cc_final: 0.8146 (t0) REVERT: G 317 ASP cc_start: 0.7787 (OUTLIER) cc_final: 0.7243 (p0) REVERT: G 384 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7174 (tt0) REVERT: G 446 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8032 (mt) REVERT: H 180 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: H 234 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.7098 (pttt) REVERT: H 258 LEU cc_start: 0.5639 (OUTLIER) cc_final: 0.5412 (mm) outliers start: 36 outliers final: 24 residues processed: 236 average time/residue: 1.4484 time to fit residues: 390.7999 Evaluate side-chains 242 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 210 time to evaluate : 2.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 428 ILE Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 441 LYS Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 620 ASN Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 589 GLU Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 347 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 7.9990 chunk 268 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 260 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN ** B 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 ASN C 318 GLN D 251 GLN D 370 ASN E 582 ASN F 494 GLN G 534 GLN H 48 GLN H 199 GLN H 233 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 23656 Z= 0.372 Angle : 0.575 8.187 32056 Z= 0.312 Chirality : 0.048 0.180 3595 Planarity : 0.004 0.049 4197 Dihedral : 5.078 29.500 3180 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.62 % Allowed : 16.11 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 2942 helix: 0.10 (0.22), residues: 571 sheet: 0.76 (0.18), residues: 757 loop : -1.44 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 374 HIS 0.002 0.000 HIS F 313 PHE 0.026 0.002 PHE C 248 TYR 0.027 0.002 TYR F 296 ARG 0.004 0.001 ARG G 457 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 201 time to evaluate : 2.701 Fit side-chains REVERT: B 281 ASP cc_start: 0.8274 (t0) cc_final: 0.8013 (t0) REVERT: B 289 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7853 (ptp-170) REVERT: B 311 ASN cc_start: 0.8621 (p0) cc_final: 0.8371 (p0) REVERT: D 463 TYR cc_start: 0.8631 (t80) cc_final: 0.8416 (t80) REVERT: E 620 ASN cc_start: 0.4110 (OUTLIER) cc_final: 0.3231 (p0) REVERT: F 218 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8311 (mp) REVERT: F 562 LEU cc_start: 0.7739 (pt) cc_final: 0.7099 (mt) REVERT: G 317 ASP cc_start: 0.7842 (OUTLIER) cc_final: 0.7544 (p0) REVERT: G 384 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: G 446 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8219 (mt) REVERT: G 489 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7529 (mttp) REVERT: H 180 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7862 (tp30) REVERT: H 234 LYS cc_start: 0.7419 (OUTLIER) cc_final: 0.7015 (ptmt) REVERT: H 258 LEU cc_start: 0.5604 (OUTLIER) cc_final: 0.5382 (mm) outliers start: 42 outliers final: 26 residues processed: 225 average time/residue: 1.5231 time to fit residues: 390.4828 Evaluate side-chains 233 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 197 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain E residue 254 LYS Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 620 ASN Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 317 ASP Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 589 GLU Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain F residue 619 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 489 LYS Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 233 ASN Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 171 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 168 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 289 optimal weight: 9.9990 chunk 266 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 178 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN B 534 GLN B 582 ASN D 251 GLN D 370 ASN E 582 ASN F 222 ASN F 494 GLN G 534 GLN H 48 GLN H 199 GLN H 233 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23656 Z= 0.262 Angle : 0.540 10.926 32056 Z= 0.293 Chirality : 0.047 0.184 3595 Planarity : 0.004 0.048 4197 Dihedral : 4.999 29.362 3180 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.50 % Allowed : 16.46 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.15), residues: 2942 helix: 0.11 (0.22), residues: 571 sheet: 0.78 (0.18), residues: 757 loop : -1.45 (0.14), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 374 HIS 0.002 0.000 HIS H 157 PHE 0.021 0.002 PHE C 248 TYR 0.024 0.001 TYR F 296 ARG 0.004 0.000 ARG G 457 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5884 Ramachandran restraints generated. 2942 Oldfield, 0 Emsley, 2942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 202 time to evaluate : 2.877 Fit side-chains REVERT: A 441 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8073 (ttpp) REVERT: B 281 ASP cc_start: 0.8243 (t0) cc_final: 0.8012 (t0) REVERT: B 289 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7818 (ptp-170) REVERT: B 311 ASN cc_start: 0.8622 (p0) cc_final: 0.8332 (p0) REVERT: D 318 GLN cc_start: 0.7535 (mt0) cc_final: 0.7311 (mt0) REVERT: D 463 TYR cc_start: 0.8610 (t80) cc_final: 0.8402 (t80) REVERT: E 620 ASN cc_start: 0.4127 (OUTLIER) cc_final: 0.3240 (p0) REVERT: F 562 LEU cc_start: 0.7653 (pt) cc_final: 0.7019 (mt) REVERT: G 317 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7519 (p0) REVERT: G 384 GLU cc_start: 0.7683 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: G 446 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8217 (mt) REVERT: H 180 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7868 (tp30) REVERT: H 234 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.6941 (pttt) REVERT: H 258 LEU cc_start: 0.5612 (OUTLIER) cc_final: 0.5390 (mm) outliers start: 39 outliers final: 25 residues processed: 223 average time/residue: 1.5314 time to fit residues: 388.8124 Evaluate side-chains 231 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 197 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ILE Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 498 GLU Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain B residue 289 ARG Chi-restraints excluded: chain B residue 310 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain D residue 451 MET Chi-restraints excluded: chain E residue 254 LYS Chi-restraints excluded: chain E residue 321 THR Chi-restraints excluded: chain E residue 620 ASN Chi-restraints excluded: chain F residue 406 THR Chi-restraints excluded: chain F residue 588 LYS Chi-restraints excluded: chain F residue 589 GLU Chi-restraints excluded: chain F residue 602 VAL Chi-restraints excluded: chain F residue 619 THR Chi-restraints excluded: chain G residue 286 LEU Chi-restraints excluded: chain G residue 317 ASP Chi-restraints excluded: chain G residue 384 GLU Chi-restraints excluded: chain G residue 446 LEU Chi-restraints excluded: chain G residue 562 LEU Chi-restraints excluded: chain G residue 571 ASP Chi-restraints excluded: chain G residue 582 ASN Chi-restraints excluded: chain H residue 180 GLU Chi-restraints excluded: chain H residue 233 ASN Chi-restraints excluded: chain H residue 234 LYS Chi-restraints excluded: chain H residue 258 LEU Chi-restraints excluded: chain H residue 285 THR Chi-restraints excluded: chain H residue 347 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 183 optimal weight: 2.9990 chunk 245 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 34 optimal weight: 0.4980 chunk 64 optimal weight: 0.9990 chunk 231 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 ASN B 582 ASN D 251 GLN D 370 ASN F 222 ASN F 494 GLN G 534 GLN H 48 GLN H 199 GLN H 233 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.120247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.086324 restraints weight = 32764.222| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 2.01 r_work: 0.2823 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23656 Z= 0.188 Angle : 0.509 9.094 32056 Z= 0.277 Chirality : 0.045 0.183 3595 Planarity : 0.004 0.046 4197 Dihedral : 4.824 28.845 3180 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.43 % Allowed : 16.54 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.15), residues: 2942 helix: 0.15 (0.22), residues: 578 sheet: 0.86 (0.18), residues: 757 loop : -1.48 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 374 HIS 0.002 0.000 HIS H 157 PHE 0.018 0.001 PHE B 248 TYR 0.021 0.001 TYR F 296 ARG 0.005 0.000 ARG C 289 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8044.25 seconds wall clock time: 145 minutes 48.40 seconds (8748.40 seconds total)