Starting phenix.real_space_refine (version: dev) on Wed Apr 6 21:53:02 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/04_2022/6klo_0713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/04_2022/6klo_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_2022/6klo_0713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/04_2022/6klo_0713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/04_2022/6klo_0713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6klo_0713/04_2022/6klo_0713.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/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: {'PTRANS': 13, 'TRANS': 353, 'PCIS': 1} 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: {'PTRANS': 13, 'TRANS': 353, 'PCIS': 1} 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: {'PTRANS': 13, 'TRANS': 353, 'PCIS': 1} 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: {'PTRANS': 13, 'TRANS': 353, 'PCIS': 1} 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: {'PTRANS': 13, 'TRANS': 353, 'PCIS': 1} 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: {'PTRANS': 13, 'TRANS': 353, 'PCIS': 1} 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: {'PTRANS': 13, 'TRANS': 353, 'PCIS': 1} 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: 13.23, per 1000 atoms: 0.57 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: 9.33 Conformation dependent library (CDL) restraints added in 3.8 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: 1.65 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: 9.28 Time building geometry restraints manager: 10.20 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 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. 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: 2.940 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: 0.020 Extract box with map and model: 15.000 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.000 Process input model: 61.380 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 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 : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 0.12 % 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 *********************** 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 : 2.817 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 363 average time/residue: 1.4006 time to fit residues: 578.1507 Evaluate side-chains 213 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 211 time to evaluate : 2.644 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.2271 time to fit residues: 4.2170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8739 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 23656 Z= 0.194 Angle : 0.523 7.475 32056 Z= 0.288 Chirality : 0.046 0.153 3595 Planarity : 0.005 0.048 4197 Dihedral : 5.178 29.507 3180 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer Outliers : 1.35 % 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: -2.09 (0.14), residues: 2942 helix: -1.05 (0.20), residues: 568 sheet: -0.64 (0.17), residues: 764 loop : -1.92 (0.13), residues: 1610 *********************** 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 270 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 235 time to evaluate : 2.974 Fit side-chains outliers start: 35 outliers final: 16 residues processed: 258 average time/residue: 1.3710 time to fit residues: 406.0022 Evaluate side-chains 221 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 205 time to evaluate : 3.039 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 5 average time/residue: 0.4669 time to fit residues: 6.9076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 146 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 264 optimal weight: 5.9990 chunk 285 optimal weight: 7.9990 chunk 235 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 264 ASN B 305 ASN B 391 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 23656 Z= 0.318 Angle : 0.553 6.560 32056 Z= 0.304 Chirality : 0.047 0.163 3595 Planarity : 0.005 0.052 4197 Dihedral : 5.302 30.622 3180 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 2.00 % 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: -1.65 (0.14), residues: 2942 helix: -0.52 (0.21), residues: 570 sheet: -0.22 (0.18), residues: 757 loop : -1.79 (0.13), residues: 1615 *********************** 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 274 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 222 time to evaluate : 2.807 Fit side-chains revert: symmetry clash outliers start: 52 outliers final: 23 residues processed: 256 average time/residue: 1.4086 time to fit residues: 411.6513 Evaluate side-chains 226 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 203 time to evaluate : 3.026 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 16 residues processed: 8 average time/residue: 0.5858 time to fit residues: 10.3682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 261 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 177 optimal weight: 0.8980 chunk 265 optimal weight: 0.9990 chunk 281 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 251 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 559 ASN E 582 ASN E 620 ASN F 222 ASN F 494 GLN F 508 GLN G 534 GLN H 199 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 23656 Z= 0.200 Angle : 0.506 7.798 32056 Z= 0.278 Chirality : 0.045 0.146 3595 Planarity : 0.004 0.048 4197 Dihedral : 5.022 28.043 3180 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer Outliers : 1.97 % 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: -1.27 (0.14), residues: 2942 helix: -0.18 (0.22), residues: 570 sheet: 0.16 (0.18), residues: 757 loop : -1.63 (0.14), residues: 1615 *********************** 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 267 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 216 time to evaluate : 2.954 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 30 residues processed: 246 average time/residue: 1.4000 time to fit residues: 397.2840 Evaluate side-chains 228 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 2.668 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 24 residues processed: 7 average time/residue: 0.6890 time to fit residues: 10.0612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 234 optimal weight: 0.5980 chunk 159 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 209 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 chunk 194 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN B 582 ASN C 318 GLN ** D 559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 582 ASN F 494 GLN G 534 GLN H 199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 23656 Z= 0.186 Angle : 0.496 7.877 32056 Z= 0.272 Chirality : 0.045 0.189 3595 Planarity : 0.004 0.048 4197 Dihedral : 4.877 27.598 3180 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 2.04 % 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: -1.07 (0.14), residues: 2942 helix: -0.02 (0.22), residues: 570 sheet: 0.39 (0.18), residues: 757 loop : -1.56 (0.14), residues: 1615 *********************** 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 268 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 215 time to evaluate : 2.895 Fit side-chains revert: symmetry clash outliers start: 53 outliers final: 33 residues processed: 248 average time/residue: 1.4133 time to fit residues: 401.8953 Evaluate side-chains 231 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 198 time to evaluate : 2.863 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 25 residues processed: 9 average time/residue: 0.5794 time to fit residues: 10.6895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 94 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 55 optimal weight: 0.9990 chunk 165 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 281 optimal weight: 2.9990 chunk 233 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 93 optimal weight: 0.0000 chunk 147 optimal weight: 0.0570 overall best weight: 0.4702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN D 251 GLN E 582 ASN F 494 GLN G 534 GLN H 48 GLN H 199 GLN ** H 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 23656 Z= 0.137 Angle : 0.471 8.133 32056 Z= 0.258 Chirality : 0.044 0.139 3595 Planarity : 0.004 0.049 4197 Dihedral : 4.600 26.301 3180 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer Outliers : 1.73 % 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: 0.11 (0.22), residues: 578 sheet: 0.67 (0.18), residues: 757 loop : -1.53 (0.14), residues: 1607 *********************** 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 275 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 230 time to evaluate : 3.077 Fit side-chains revert: symmetry clash outliers start: 45 outliers final: 27 residues processed: 260 average time/residue: 1.3618 time to fit residues: 414.3351 Evaluate side-chains 229 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 202 time to evaluate : 2.623 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 21 residues processed: 7 average time/residue: 0.4451 time to fit residues: 8.6289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 271 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 chunk 160 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 237 optimal weight: 1.9990 chunk 157 optimal weight: 4.9990 chunk 280 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 170 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN D 251 GLN E 367 GLN E 582 ASN F 494 GLN G 534 GLN H 48 GLN H 233 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 23656 Z= 0.270 Angle : 0.528 7.962 32056 Z= 0.289 Chirality : 0.046 0.153 3595 Planarity : 0.005 0.128 4197 Dihedral : 4.928 27.819 3180 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 1.54 % 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: -0.86 (0.14), residues: 2942 helix: 0.07 (0.22), residues: 577 sheet: 0.75 (0.18), residues: 750 loop : -1.52 (0.14), residues: 1615 *********************** 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 247 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 207 time to evaluate : 3.055 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 30 residues processed: 236 average time/residue: 1.5016 time to fit residues: 408.8559 Evaluate side-chains 230 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 200 time to evaluate : 2.933 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 23 residues processed: 7 average time/residue: 0.3754 time to fit residues: 7.7950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 173 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 178 optimal weight: 0.0030 chunk 191 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 220 optimal weight: 3.9990 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN D 251 GLN E 582 ASN F 494 GLN G 534 GLN H 48 GLN H 199 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.062 23656 Z= 0.201 Angle : 0.499 8.449 32056 Z= 0.273 Chirality : 0.045 0.155 3595 Planarity : 0.004 0.115 4197 Dihedral : 4.830 27.389 3180 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 1.46 % 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: -0.82 (0.15), residues: 2942 helix: 0.11 (0.22), residues: 578 sheet: 0.78 (0.18), residues: 757 loop : -1.51 (0.14), residues: 1607 *********************** 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 244 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 206 time to evaluate : 3.098 Fit side-chains revert: symmetry clash outliers start: 38 outliers final: 29 residues processed: 235 average time/residue: 1.3521 time to fit residues: 366.6213 Evaluate side-chains 220 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 2.735 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 26 residues processed: 3 average time/residue: 0.5395 time to fit residues: 5.8427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 291 random chunks: chunk 255 optimal weight: 2.9990 chunk 268 optimal weight: 6.9990 chunk 245 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 157 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 chunk 247 optimal weight: 1.9990 chunk 260 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN D 251 GLN D 370 ASN E 582 ASN F 494 GLN G 534 GLN H 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 23656 Z= 0.265 Angle : 0.528 8.329 32056 Z= 0.290 Chirality : 0.046 0.182 3595 Planarity : 0.004 0.094 4197 Dihedral : 4.955 28.080 3180 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer Outliers : 1.50 % 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: -0.85 (0.14), residues: 2942 helix: 0.08 (0.22), residues: 578 sheet: 0.75 (0.18), residues: 757 loop : -1.52 (0.14), residues: 1607 *********************** 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 240 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 201 time to evaluate : 3.201 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 34 residues processed: 231 average time/residue: 1.3567 time to fit residues: 363.7338 Evaluate side-chains 228 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 194 time to evaluate : 2.960 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 26 residues processed: 8 average time/residue: 0.6475 time to fit residues: 10.7024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 168 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 289 optimal weight: 9.9990 chunk 266 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 178 optimal weight: 2.9990 chunk 141 optimal weight: 0.0970 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 582 ASN D 251 GLN D 370 ASN E 582 ASN F 494 GLN G 534 GLN H 48 GLN H 199 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 23656 Z= 0.212 Angle : 0.513 8.496 32056 Z= 0.280 Chirality : 0.046 0.164 3595 Planarity : 0.004 0.088 4197 Dihedral : 4.865 27.894 3180 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer Outliers : 1.35 % 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: -0.80 (0.15), residues: 2942 helix: 0.13 (0.22), residues: 578 sheet: 0.77 (0.18), residues: 767 loop : -1.50 (0.14), residues: 1597 ********************** 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 235 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 200 time to evaluate : 2.859 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 32 residues processed: 228 average time/residue: 1.3608 time to fit residues: 357.7312 Evaluate side-chains 224 residues out of total 2594 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 192 time to evaluate : 2.926 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 27 residues processed: 5 average time/residue: 0.6466 time to fit residues: 8.0092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 212 optimal weight: 6.9990 chunk 34 optimal weight: 0.0980 chunk 64 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 237 optimal weight: 0.0770 chunk 29 optimal weight: 0.0070 chunk 42 optimal weight: 0.5980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 ASN B 582 ASN D 251 GLN D 370 ASN F 494 GLN G 534 GLN H 48 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.122822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.089264 restraints weight = 32709.527| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 2.01 r_work: 0.2972 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 1.80 restraints_weight: 0.2500 r_work: 0.2947 rms_B_bonded: 1.83 restraints_weight: 0.1250 r_work: 0.2934 rms_B_bonded: 1.91 restraints_weight: 0.0625 r_work: 0.2920 rms_B_bonded: 2.03 restraints_weight: 0.0312 r_work: 0.2905 rms_B_bonded: 2.18 restraints_weight: 0.0156 r_work: 0.2889 rms_B_bonded: 2.36 restraints_weight: 0.0078 r_work: 0.2872 rms_B_bonded: 2.59 restraints_weight: 0.0039 r_work: 0.2853 rms_B_bonded: 2.85 restraints_weight: 0.0020 r_work: 0.2832 rms_B_bonded: 3.17 restraints_weight: 0.0010 r_work: 0.2809 rms_B_bonded: 3.54 restraints_weight: 0.0005 r_work: 0.2784 rms_B_bonded: 3.96 restraints_weight: 0.0002 r_work: 0.2757 rms_B_bonded: 4.45 restraints_weight: 0.0001 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 23656 Z= 0.132 Angle : 0.474 9.199 32056 Z= 0.258 Chirality : 0.044 0.154 3595 Planarity : 0.004 0.083 4197 Dihedral : 4.433 25.865 3180 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 1.31 % 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: -0.62 (0.15), residues: 2942 helix: 0.24 (0.22), residues: 578 sheet: 1.00 (0.18), residues: 757 loop : -1.42 (0.14), residues: 1607 =============================================================================== Job complete usr+sys time: 6732.16 seconds wall clock time: 121 minutes 47.35 seconds (7307.35 seconds total)