Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 12:45:53 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrj_22446/04_2023/7jrj_22446.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrj_22446/04_2023/7jrj_22446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrj_22446/04_2023/7jrj_22446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrj_22446/04_2023/7jrj_22446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrj_22446/04_2023/7jrj_22446.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrj_22446/04_2023/7jrj_22446.pdb" } resolution = 3.03 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 67 5.16 5 C 14587 2.51 5 N 3924 2.21 5 O 4346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 466": "NH1" <-> "NH2" Residue "F PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 526": "NH1" <-> "NH2" Residue "F ARG 568": "NH1" <-> "NH2" Residue "F TYR 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 604": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 666": "NH1" <-> "NH2" Residue "F ARG 670": "NH1" <-> "NH2" Residue "F GLU 685": "OE1" <-> "OE2" Residue "F ARG 697": "NH1" <-> "NH2" Residue "F ARG 712": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 88": "NH1" <-> "NH2" Residue "K PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 191": "NH1" <-> "NH2" Residue "I PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 309": "NH1" <-> "NH2" Residue "I ARG 329": "NH1" <-> "NH2" Residue "I ARG 506": "NH1" <-> "NH2" Residue "I PHE 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 29": "NH1" <-> "NH2" Residue "H ARG 92": "NH1" <-> "NH2" Residue "H TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 263": "NH1" <-> "NH2" Residue "H ARG 265": "NH1" <-> "NH2" Residue "H ARG 332": "NH1" <-> "NH2" Residue "H ARG 366": "NH1" <-> "NH2" Residue "H TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 430": "NH1" <-> "NH2" Residue "H ARG 469": "NH1" <-> "NH2" Residue "H ARG 473": "NH1" <-> "NH2" Residue "H PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 107": "NH1" <-> "NH2" Residue "A ARG 216": "NH1" <-> "NH2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ARG 107": "NH1" <-> "NH2" Residue "B ARG 216": "NH1" <-> "NH2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 444": "OE1" <-> "OE2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 138": "NH1" <-> "NH2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ARG 387": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 22924 Number of models: 1 Model: "" Number of chains: 15 Chain: "E" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1378 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 171} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 2658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 356, 2658 Classifications: {'peptide': 356} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 2, 'PTRANS': 26, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1232 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 10, 'TRANS': 147} Chain: "I" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2517 Classifications: {'peptide': 327} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 21, 'TRANS': 305} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 19 Classifications: {'peptide': 4} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 4} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1094 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 145} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3611 Classifications: {'peptide': 477} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 439} Chain breaks: 3 Chain: "A" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1955 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 11, 'TRANS': 240} Chain breaks: 1 Chain: "B" Number of atoms: 1955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 1955 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 11, 'TRANS': 240} Chain breaks: 1 Chain: "C" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2717 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 329} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3168 Classifications: {'peptide': 422} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 377} Chain breaks: 1 Chain: "L" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Classifications: {'peptide': 6} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'TRANS': 5} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'UNK:plan-1': 6} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 25 Classifications: {'peptide': 5} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'UNK:plan-1': 5} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 320 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'TRANS': 63} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 192 Unresolved non-hydrogen dihedrals: 64 Planarities with less than four sites: {'UNK:plan-1': 64} Unresolved non-hydrogen planarities: 64 Chain: "O" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 245 Classifications: {'peptide': 49} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 98 Unresolved non-hydrogen angles: 147 Unresolved non-hydrogen dihedrals: 49 Planarities with less than four sites: {'UNK:plan-1': 49} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 11.42, per 1000 atoms: 0.50 Number of scatterers: 22924 At special positions: 0 Unit cell: (131.095, 153.64, 259.685, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 67 16.00 O 4346 8.00 N 3924 7.00 C 14587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 105 " - pdb=" SG CYS A 155 " distance=2.29 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: 8.28 Conformation dependent library (CDL) restraints added in 3.4 seconds 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5610 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 27 sheets defined 39.6% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'F' and resid 460 through 467 Processing helix chain 'F' and resid 472 through 477 Processing helix chain 'F' and resid 480 through 512 removed outlier: 3.596A pdb=" N SER F 512 " --> pdb=" O ALA F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 541 Processing helix chain 'F' and resid 542 through 552 Processing helix chain 'F' and resid 720 through 725 removed outlier: 3.790A pdb=" N ILE F 724 " --> pdb=" O ALA F 720 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLN F 725 " --> pdb=" O ALA F 721 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 720 through 725' Processing helix chain 'K' and resid 12 through 18 Processing helix chain 'K' and resid 20 through 31 Processing helix chain 'K' and resid 44 through 52 Processing helix chain 'K' and resid 53 through 56 removed outlier: 3.931A pdb=" N LYS K 56 " --> pdb=" O GLY K 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 53 through 56' Processing helix chain 'K' and resid 60 through 66 Processing helix chain 'K' and resid 82 through 92 removed outlier: 3.670A pdb=" N ALA K 86 " --> pdb=" O GLY K 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG K 88 " --> pdb=" O ILE K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 103 Processing helix chain 'K' and resid 107 through 112 Processing helix chain 'K' and resid 125 through 137 Processing helix chain 'K' and resid 143 through 148 Processing helix chain 'K' and resid 151 through 161 removed outlier: 3.547A pdb=" N GLU K 155 " --> pdb=" O THR K 151 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 31 Processing helix chain 'I' and resid 35 through 98 removed outlier: 3.512A pdb=" N TYR I 39 " --> pdb=" O ASP I 35 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU I 52 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY I 55 " --> pdb=" O ALA I 51 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU I 79 " --> pdb=" O GLU I 75 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA I 82 " --> pdb=" O SER I 78 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU I 98 " --> pdb=" O ASP I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 118 Processing helix chain 'I' and resid 194 through 198 removed outlier: 4.172A pdb=" N LYS I 197 " --> pdb=" O ASP I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 210 through 214 Processing helix chain 'I' and resid 237 through 239 No H-bonds generated for 'chain 'I' and resid 237 through 239' Processing helix chain 'I' and resid 240 through 245 Processing helix chain 'I' and resid 254 through 258 Processing helix chain 'I' and resid 305 through 333 Processing helix chain 'I' and resid 462 through 475 removed outlier: 3.574A pdb=" N HIS I 475 " --> pdb=" O LEU I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 475 through 485 Processing helix chain 'I' and resid 490 through 504 removed outlier: 3.663A pdb=" N HIS I 495 " --> pdb=" O GLN I 491 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL I 496 " --> pdb=" O GLY I 492 " (cutoff:3.500A) Processing helix chain 'I' and resid 513 through 518 Processing helix chain 'I' and resid 523 through 531 Processing helix chain 'G' and resid 281 through 353 removed outlier: 3.696A pdb=" N GLN G 285 " --> pdb=" O TRP G 281 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA G 309 " --> pdb=" O GLU G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 353 through 360 Processing helix chain 'G' and resid 369 through 389 removed outlier: 3.822A pdb=" N GLU G 373 " --> pdb=" O ALA G 369 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN G 382 " --> pdb=" O GLU G 378 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA G 383 " --> pdb=" O LEU G 379 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU G 384 " --> pdb=" O THR G 380 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU G 385 " --> pdb=" O ALA G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 471 through 483 Processing helix chain 'G' and resid 486 through 499 Processing helix chain 'H' and resid 20 through 26 Processing helix chain 'H' and resid 52 through 57 Processing helix chain 'H' and resid 84 through 95 removed outlier: 3.691A pdb=" N ASN H 88 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N LEU H 90 " --> pdb=" O GLU H 86 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N VAL H 91 " --> pdb=" O TYR H 87 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG H 92 " --> pdb=" O ASN H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 117 removed outlier: 3.563A pdb=" N ARG H 101 " --> pdb=" O THR H 97 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN H 112 " --> pdb=" O ILE H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 156 removed outlier: 3.831A pdb=" N PHE H 153 " --> pdb=" O VAL H 149 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N SER H 154 " --> pdb=" O LYS H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 161 through 173 Processing helix chain 'H' and resid 189 through 194 Processing helix chain 'H' and resid 207 through 226 Processing helix chain 'H' and resid 242 through 249 removed outlier: 3.605A pdb=" N GLY H 249 " --> pdb=" O TRP H 245 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 269 removed outlier: 3.619A pdb=" N ALA H 255 " --> pdb=" O PRO H 251 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL H 257 " --> pdb=" O ALA H 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 310 Processing helix chain 'H' and resid 342 through 350 Processing helix chain 'H' and resid 368 through 378 removed outlier: 3.704A pdb=" N LEU H 372 " --> pdb=" O ALA H 368 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS H 377 " --> pdb=" O ASP H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 414 through 426 Processing helix chain 'H' and resid 427 through 445 removed outlier: 3.799A pdb=" N VAL H 437 " --> pdb=" O ALA H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 448 through 459 removed outlier: 3.759A pdb=" N VAL H 452 " --> pdb=" O LYS H 448 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA H 453 " --> pdb=" O PRO H 449 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU H 454 " --> pdb=" O GLU H 450 " (cutoff:3.500A) Processing helix chain 'H' and resid 485 through 490 Processing helix chain 'H' and resid 496 through 500 removed outlier: 3.707A pdb=" N LEU H 499 " --> pdb=" O ASP H 496 " (cutoff:3.500A) Processing helix chain 'H' and resid 507 through 515 Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 23 through 41 Proline residue: A 35 - end of helix Processing helix chain 'A' and resid 98 through 108 removed outlier: 3.582A pdb=" N THR A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG A 104 " --> pdb=" O GLU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 164 Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 264 through 269 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 23 through 41 Proline residue: B 35 - end of helix Processing helix chain 'B' and resid 98 through 108 removed outlier: 3.583A pdb=" N THR B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG B 104 " --> pdb=" O GLU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 164 Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 210 through 214 Processing helix chain 'B' and resid 264 through 269 Processing helix chain 'C' and resid 7 through 15 removed outlier: 3.595A pdb=" N GLN C 15 " --> pdb=" O LEU C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 40 removed outlier: 3.597A pdb=" N GLU C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 56 Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 130 through 145 Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 266 through 283 removed outlier: 3.624A pdb=" N ALA C 281 " --> pdb=" O ARG C 277 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 439 through 443 Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 22 through 37 Processing helix chain 'D' and resid 41 through 49 removed outlier: 4.474A pdb=" N GLU D 47 " --> pdb=" O VAL D 43 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR D 48 " --> pdb=" O GLU D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 109 through 121 Processing helix chain 'D' and resid 125 through 142 Processing helix chain 'D' and resid 191 through 196 removed outlier: 3.551A pdb=" N ASN D 194 " --> pdb=" O GLU D 191 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA D 195 " --> pdb=" O GLY D 192 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR D 196 " --> pdb=" O VAL D 193 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 191 through 196' Processing helix chain 'D' and resid 215 through 223 Processing helix chain 'D' and resid 246 through 263 removed outlier: 3.637A pdb=" N ALA D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL D 263 " --> pdb=" O SER D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 297 removed outlier: 4.152A pdb=" N GLU D 292 " --> pdb=" O LYS D 289 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET D 293 " --> pdb=" O GLY D 290 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU D 295 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Proline residue: D 296 - end of helix Processing helix chain 'D' and resid 333 through 337 removed outlier: 3.739A pdb=" N GLU D 337 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 349 removed outlier: 3.704A pdb=" N ASP D 349 " --> pdb=" O LEU D 346 " (cutoff:3.500A) Processing helix chain 'O' and resid 352 through 372 removed outlier: 3.789A pdb=" N UNK O 357 " --> pdb=" O UNK O 353 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N UNK O 360 " --> pdb=" O UNK O 356 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N UNK O 362 " --> pdb=" O UNK O 358 " (cutoff:3.500A) Processing helix chain 'O' and resid 802 through 806 removed outlier: 3.764A pdb=" N UNK O 806 " --> pdb=" O UNK O 803 " (cutoff:3.500A) Processing helix chain 'O' and resid 808 through 811 removed outlier: 3.819A pdb=" N UNK O 811 " --> pdb=" O UNK O 808 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 808 through 811' Processing helix chain 'O' and resid 812 through 823 removed outlier: 3.691A pdb=" N UNK O 822 " --> pdb=" O UNK O 818 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 201 through 203 Processing sheet with id=AA2, first strand: chain 'E' and resid 201 through 203 removed outlier: 7.376A pdb=" N THR E 178 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY E 154 " --> pdb=" O GLY E 166 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N THR E 152 " --> pdb=" O PHE E 168 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ASP E 145 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY E 154 " --> pdb=" O VAL E 143 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL E 143 " --> pdb=" O GLY E 154 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N TRP E 156 " --> pdb=" O GLN E 141 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N GLN E 141 " --> pdb=" O TRP E 156 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N HIS E 128 " --> pdb=" O TRP E 123 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TRP E 123 " --> pdb=" O HIS E 128 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LYS E 130 " --> pdb=" O ALA E 121 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N GLN E 107 " --> pdb=" O ASP E 98 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLY E 97 " --> pdb=" O GLY E 85 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N HIS E 82 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N VAL E 77 " --> pdb=" O HIS E 82 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LYS E 84 " --> pdb=" O ASP E 75 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP E 75 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY E 59 " --> pdb=" O TYR E 76 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL E 56 " --> pdb=" O GLU E 53 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR E 58 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N THR E 51 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS E 60 " --> pdb=" O GLU E 49 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU E 49 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N THR E 62 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N LYS E 47 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE E 48 " --> pdb=" O MET E 28 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET E 28 " --> pdb=" O PHE E 48 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU E 29 " --> pdb=" O UNK M -3 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N UNK M -3 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 523 through 528 removed outlier: 3.790A pdb=" N LYS F 452 " --> pdb=" O ARG F 528 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N UNK N -7 " --> pdb=" O UNK N -54 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N UNK N -57 " --> pdb=" O UNK N -45 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N UNK N -45 " --> pdb=" O UNK N -57 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N UNK N -55 " --> pdb=" O UNK N -47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 564 through 570 removed outlier: 3.573A pdb=" N SER F 564 " --> pdb=" O TYR F 581 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR F 566 " --> pdb=" O GLY F 579 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY F 579 " --> pdb=" O THR F 566 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG F 568 " --> pdb=" O TYR F 577 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR F 577 " --> pdb=" O ARG F 568 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU F 603 " --> pdb=" O HIS F 610 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 585 through 586 removed outlier: 3.645A pdb=" N VAL F 585 " --> pdb=" O ALA F 582 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLN F 635 " --> pdb=" O GLU F 626 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL F 628 " --> pdb=" O GLU F 633 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLU F 633 " --> pdb=" O VAL F 628 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER F 649 " --> pdb=" O PRO F 658 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY F 659 " --> pdb=" O GLY F 671 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY F 671 " --> pdb=" O GLY F 659 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 677 " --> pdb=" O LYS F 674 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 680 through 686 removed outlier: 6.419A pdb=" N ARG F 690 " --> pdb=" O THR F 705 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR F 705 " --> pdb=" O ARG F 690 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU F 692 " --> pdb=" O THR F 703 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR F 703 " --> pdb=" O GLU F 692 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU F 694 " --> pdb=" O ALA F 701 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 708 " --> pdb=" O LEU F 732 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 680 through 686 removed outlier: 6.419A pdb=" N ARG F 690 " --> pdb=" O THR F 705 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR F 705 " --> pdb=" O ARG F 690 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N GLU F 692 " --> pdb=" O THR F 703 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N THR F 703 " --> pdb=" O GLU F 692 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU F 694 " --> pdb=" O ALA F 701 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU F 708 " --> pdb=" O LEU F 732 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 5 through 11 removed outlier: 3.774A pdb=" N GLU K 5 " --> pdb=" O LYS K 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU K 76 " --> pdb=" O ALA K 9 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE K 73 " --> pdb=" O LYS K 40 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N LYS K 40 " --> pdb=" O ILE K 73 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA K 75 " --> pdb=" O LYS K 38 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LYS K 38 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL K 77 " --> pdb=" O ILE K 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 216 through 217 removed outlier: 6.783A pdb=" N ALA I 125 " --> pdb=" O VAL I 203 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ALA I 205 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA I 123 " --> pdb=" O ALA I 205 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS I 287 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL I 278 " --> pdb=" O LYS I 287 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LEU I 289 " --> pdb=" O CYS I 276 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N CYS I 276 " --> pdb=" O LEU I 289 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA I 291 " --> pdb=" O GLN I 274 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLN I 274 " --> pdb=" O ALA I 291 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 32 through 35 removed outlier: 5.376A pdb=" N GLU H 33 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU H 40 " --> pdb=" O GLU H 33 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU H 35 " --> pdb=" O VAL H 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 381 through 384 removed outlier: 6.713A pdb=" N ILE H 334 " --> pdb=" O CYS H 356 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N GLN H 358 " --> pdb=" O ILE H 334 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU H 336 " --> pdb=" O GLN H 358 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL H 287 " --> pdb=" O GLY H 335 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL H 337 " --> pdb=" O VAL H 287 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU H 289 " --> pdb=" O VAL H 337 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU H 286 " --> pdb=" O LEU H 232 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N LYS H 235 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL H 44 " --> pdb=" O VAL H 466 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 313 through 315 removed outlier: 6.575A pdb=" N GLN H 313 " --> pdb=" O SER H 326 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 92 through 93 removed outlier: 6.028A pdb=" N GLU A 64 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU A 48 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TYR A 66 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU A 46 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 16.266A pdb=" N TRP A 251 " --> pdb=" O SER A 45 " (cutoff:3.500A) removed outlier: 11.365A pdb=" N THR A 47 " --> pdb=" O TRP A 251 " (cutoff:3.500A) removed outlier: 9.999A pdb=" N SER A 253 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TRP A 49 " --> pdb=" O SER A 253 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TYR A 240 " --> pdb=" O SER A 234 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 75 through 78 removed outlier: 4.505A pdb=" N ALA A 69 " --> pdb=" O VAL A 180 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 119 through 124 Processing sheet with id=AB7, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AB8, first strand: chain 'B' and resid 92 through 93 removed outlier: 6.028A pdb=" N GLU B 64 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU B 48 " --> pdb=" O GLU B 64 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N TYR B 66 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU B 46 " --> pdb=" O TYR B 66 " (cutoff:3.500A) removed outlier: 16.265A pdb=" N TRP B 251 " --> pdb=" O SER B 45 " (cutoff:3.500A) removed outlier: 11.365A pdb=" N THR B 47 " --> pdb=" O TRP B 251 " (cutoff:3.500A) removed outlier: 9.998A pdb=" N SER B 253 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TRP B 49 " --> pdb=" O SER B 253 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N TYR B 240 " --> pdb=" O SER B 234 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 75 through 78 removed outlier: 4.506A pdb=" N ALA B 69 " --> pdb=" O VAL B 180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 119 through 124 Processing sheet with id=AC2, first strand: chain 'B' and resid 166 through 168 Processing sheet with id=AC3, first strand: chain 'C' and resid 229 through 230 removed outlier: 6.561A pdb=" N TYR C 167 " --> pdb=" O LYS C 159 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LYS C 159 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL C 169 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 12.037A pdb=" N ARG C 155 " --> pdb=" O TRP C 412 " (cutoff:3.500A) removed outlier: 10.687A pdb=" N CYS C 414 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N PHE C 157 " --> pdb=" O CYS C 414 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N ALA C 403 " --> pdb=" O SER C 397 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 284 through 286 Processing sheet with id=AC5, first strand: chain 'C' and resid 290 through 293 Processing sheet with id=AC6, first strand: chain 'D' and resid 209 through 210 removed outlier: 6.829A pdb=" N TYR D 163 " --> pdb=" O GLY D 154 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY D 154 " --> pdb=" O TYR D 163 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL D 165 " --> pdb=" O PHE D 152 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N PHE D 152 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU D 167 " --> pdb=" O VAL D 150 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N VAL D 150 " --> pdb=" O GLU D 167 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N THR D 169 " --> pdb=" O SER D 148 " (cutoff:3.500A) removed outlier: 22.559A pdb=" N PHE D 400 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 16.439A pdb=" N THR D 149 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 14.877A pdb=" N SER D 402 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N ARG D 151 " --> pdb=" O SER D 402 " (cutoff:3.500A) removed outlier: 9.650A pdb=" N TYR D 404 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N PHE D 153 " --> pdb=" O TYR D 404 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N GLY D 406 " --> pdb=" O PHE D 153 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LYS D 155 " --> pdb=" O GLY D 406 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ALA D 391 " --> pdb=" O SER D 385 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA D 381 " --> pdb=" O CYS D 395 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 382 " --> pdb=" O VAL D 368 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 264 through 266 Processing sheet with id=AC8, first strand: chain 'D' and resid 270 through 272 Processing sheet with id=AC9, first strand: chain 'N' and resid -73 through -71 removed outlier: 3.555A pdb=" N UNK N -83 " --> pdb=" O UNK N -25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N UNK N -81 " --> pdb=" O UNK N -27 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N UNK N -27 " --> pdb=" O UNK N -81 " (cutoff:3.500A) 1088 hydrogen bonds defined for protein. 3027 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: 8.54 Time building geometry restraints manager: 8.96 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: 7609 1.34 - 1.46: 3861 1.46 - 1.57: 11881 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 23455 Sorted by residual: bond pdb=" N VAL H 495 " pdb=" CA VAL H 495 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.18e-02 7.18e+03 9.90e+00 bond pdb=" N GLY H 497 " pdb=" CA GLY H 497 " ideal model delta sigma weight residual 1.443 1.477 -0.035 1.37e-02 5.33e+03 6.37e+00 bond pdb=" N ASP H 496 " pdb=" CA ASP H 496 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.18e+00 bond pdb=" N CYS B 155 " pdb=" CA CYS B 155 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.93e+00 bond pdb=" N ARG B 154 " pdb=" CA ARG B 154 " ideal model delta sigma weight residual 1.459 1.481 -0.022 1.21e-02 6.83e+03 3.29e+00 ... (remaining 23450 not shown) Histogram of bond angle deviations from ideal: 99.25 - 106.21: 831 106.21 - 113.17: 12577 113.17 - 120.13: 8196 120.13 - 127.08: 9986 127.08 - 134.04: 326 Bond angle restraints: 31916 Sorted by residual: angle pdb=" C ALA B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 122.44 117.92 4.52 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C ALA A 163 " pdb=" N THR A 164 " pdb=" CA THR A 164 " ideal model delta sigma weight residual 122.44 117.94 4.50 1.19e+00 7.06e-01 1.43e+01 angle pdb=" C GLU F 685 " pdb=" N GLN F 686 " pdb=" CA GLN F 686 " ideal model delta sigma weight residual 122.07 127.28 -5.21 1.44e+00 4.82e-01 1.31e+01 angle pdb=" CA GLN F 686 " pdb=" C GLN F 686 " pdb=" N PRO F 687 " ideal model delta sigma weight residual 117.68 120.19 -2.51 7.10e-01 1.98e+00 1.25e+01 angle pdb=" N THR B 164 " pdb=" CA THR B 164 " pdb=" C THR B 164 " ideal model delta sigma weight residual 111.02 116.16 -5.14 1.52e+00 4.33e-01 1.14e+01 ... (remaining 31911 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 13213 17.93 - 35.86: 614 35.86 - 53.79: 114 53.79 - 71.73: 18 71.73 - 89.66: 11 Dihedral angle restraints: 13970 sinusoidal: 5230 harmonic: 8740 Sorted by residual: dihedral pdb=" CA LEU I 295 " pdb=" C LEU I 295 " pdb=" N PHE I 296 " pdb=" CA PHE I 296 " ideal model delta harmonic sigma weight residual -180.00 -151.30 -28.70 0 5.00e+00 4.00e-02 3.30e+01 dihedral pdb=" CA TRP H 470 " pdb=" C TRP H 470 " pdb=" N SER H 471 " pdb=" CA SER H 471 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLU D 325 " pdb=" C GLU D 325 " pdb=" N PRO D 326 " pdb=" CA PRO D 326 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 13967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 2368 0.037 - 0.075: 870 0.075 - 0.112: 224 0.112 - 0.150: 57 0.150 - 0.187: 4 Chirality restraints: 3523 Sorted by residual: chirality pdb=" CB VAL H 495 " pdb=" CA VAL H 495 " pdb=" CG1 VAL H 495 " pdb=" CG2 VAL H 495 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA PHE I 296 " pdb=" N PHE I 296 " pdb=" C PHE I 296 " pdb=" CB PHE I 296 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA PRO F 687 " pdb=" N PRO F 687 " pdb=" C PRO F 687 " pdb=" CB PRO F 687 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 3520 not shown) Planarity restraints: 4196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 325 " -0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO D 326 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO D 326 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 326 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 686 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO F 687 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO F 687 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 687 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU F 765 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO F 766 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO F 766 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 766 " -0.023 5.00e-02 4.00e+02 ... (remaining 4193 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3191 2.75 - 3.29: 21368 3.29 - 3.82: 36424 3.82 - 4.36: 44063 4.36 - 4.90: 75949 Nonbonded interactions: 180995 Sorted by model distance: nonbonded pdb=" OH TYR H 480 " pdb=" OD1 ASP H 496 " model vdw 2.210 2.440 nonbonded pdb=" OG SER F 580 " pdb=" O HIS F 587 " model vdw 2.230 2.440 nonbonded pdb=" OG SER F 807 " pdb=" OG1 THR F 810 " model vdw 2.231 2.440 nonbonded pdb=" OD2 ASP G 306 " pdb=" OH TYR D 24 " model vdw 2.234 2.440 nonbonded pdb=" OG SER K 123 " pdb=" OE1 GLU K 132 " model vdw 2.235 2.440 ... (remaining 180990 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' } 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: 8.330 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: 35.590 Check model and map are aligned: 0.430 Set scattering table: 0.190 Process input model: 55.690 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.110 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 23455 Z= 0.400 Angle : 0.599 8.005 31916 Z= 0.335 Chirality : 0.042 0.187 3523 Planarity : 0.004 0.058 4196 Dihedral : 11.334 89.658 8357 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: -2.44 (0.14), residues: 2879 helix: -1.05 (0.14), residues: 1018 sheet: -1.33 (0.22), residues: 519 loop : -2.14 (0.15), residues: 1342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 313 average time/residue: 0.4252 time to fit residues: 194.4472 Evaluate side-chains 151 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 2.573 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2024 time to fit residues: 3.7492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 0.5980 chunk 225 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 120 optimal weight: 0.5980 chunk 233 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 270 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 141 GLN ** E 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 533 ASN F 544 HIS F 548 ASN F 686 GLN F 723 HIS F 725 GLN K 31 ASN K 55 HIS I 254 ASN H 267 ASN H 361 HIS A 3 GLN ** A 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN B 3 GLN B 14 HIS B 27 GLN B 247 ASN C 269 ASN D 173 ASN D 305 HIS D 426 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23455 Z= 0.164 Angle : 0.527 7.063 31916 Z= 0.269 Chirality : 0.039 0.186 3523 Planarity : 0.004 0.051 4196 Dihedral : 4.110 26.199 3267 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: -0.89 (0.15), residues: 2879 helix: 0.49 (0.16), residues: 1034 sheet: -0.81 (0.23), residues: 520 loop : -1.33 (0.16), residues: 1325 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 12 residues processed: 194 average time/residue: 0.3763 time to fit residues: 112.8844 Evaluate side-chains 162 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 150 time to evaluate : 2.341 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2371 time to fit residues: 8.5931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 0.4980 chunk 83 optimal weight: 0.0370 chunk 225 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 271 optimal weight: 3.9990 chunk 292 optimal weight: 20.0000 chunk 241 optimal weight: 1.9990 chunk 268 optimal weight: 0.0870 chunk 92 optimal weight: 9.9990 chunk 217 optimal weight: 3.9990 overall best weight: 1.3240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 518 HIS H 109 GLN A 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 23455 Z= 0.205 Angle : 0.529 10.381 31916 Z= 0.267 Chirality : 0.040 0.183 3523 Planarity : 0.004 0.049 4196 Dihedral : 4.006 25.210 3267 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: -0.29 (0.15), residues: 2879 helix: 1.02 (0.16), residues: 1035 sheet: -0.50 (0.23), residues: 512 loop : -1.00 (0.16), residues: 1332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 156 time to evaluate : 2.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 14 residues processed: 174 average time/residue: 0.3829 time to fit residues: 103.4474 Evaluate side-chains 153 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 2.684 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2286 time to fit residues: 9.4615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 0.9990 chunk 203 optimal weight: 0.2980 chunk 140 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 129 optimal weight: 0.4980 chunk 182 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 288 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN D 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 23455 Z= 0.215 Angle : 0.523 8.377 31916 Z= 0.265 Chirality : 0.040 0.206 3523 Planarity : 0.004 0.047 4196 Dihedral : 3.990 25.005 3267 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 1.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: 0.02 (0.16), residues: 2879 helix: 1.30 (0.16), residues: 1026 sheet: -0.33 (0.23), residues: 525 loop : -0.83 (0.17), residues: 1328 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 5 residues processed: 163 average time/residue: 0.3868 time to fit residues: 98.0386 Evaluate side-chains 141 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 2.600 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2001 time to fit residues: 5.3556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 214 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 245 optimal weight: 0.0000 chunk 199 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 258 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 637 GLN I 520 HIS H 22 ASN H 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 23455 Z= 0.295 Angle : 0.573 7.756 31916 Z= 0.291 Chirality : 0.042 0.204 3523 Planarity : 0.005 0.051 4196 Dihedral : 4.210 26.550 3267 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: -0.05 (0.16), residues: 2879 helix: 1.21 (0.16), residues: 1035 sheet: -0.40 (0.23), residues: 526 loop : -0.84 (0.17), residues: 1318 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 143 time to evaluate : 2.939 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 161 average time/residue: 0.3887 time to fit residues: 98.8350 Evaluate side-chains 144 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 132 time to evaluate : 2.744 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2176 time to fit residues: 8.6382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 0.9980 chunk 259 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 288 optimal weight: 30.0000 chunk 239 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 95 optimal weight: 0.0170 chunk 151 optimal weight: 1.9990 overall best weight: 0.9620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 520 HIS H 104 ASN H 109 GLN H 477 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 23455 Z= 0.164 Angle : 0.509 8.046 31916 Z= 0.256 Chirality : 0.039 0.209 3523 Planarity : 0.004 0.043 4196 Dihedral : 3.946 24.290 3267 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: 0.32 (0.16), residues: 2879 helix: 1.54 (0.16), residues: 1031 sheet: -0.25 (0.23), residues: 527 loop : -0.62 (0.17), residues: 1321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 2.775 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 155 average time/residue: 0.3854 time to fit residues: 92.7082 Evaluate side-chains 144 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 138 time to evaluate : 2.689 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2225 time to fit residues: 6.1420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 0.0970 chunk 32 optimal weight: 10.0000 chunk 164 optimal weight: 0.5980 chunk 210 optimal weight: 0.0470 chunk 163 optimal weight: 0.9990 chunk 242 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 287 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 520 HIS H 109 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 23455 Z= 0.132 Angle : 0.481 8.392 31916 Z= 0.240 Chirality : 0.038 0.201 3523 Planarity : 0.004 0.073 4196 Dihedral : 3.699 22.180 3267 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: 0.64 (0.16), residues: 2879 helix: 1.83 (0.16), residues: 1036 sheet: -0.06 (0.24), residues: 511 loop : -0.45 (0.17), residues: 1332 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 145 time to evaluate : 2.676 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 149 average time/residue: 0.4062 time to fit residues: 93.2537 Evaluate side-chains 139 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 135 time to evaluate : 2.536 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2365 time to fit residues: 5.2807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 26 optimal weight: 9.9990 chunk 225 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN I 520 HIS H 104 ASN H 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 23455 Z= 0.195 Angle : 0.505 8.156 31916 Z= 0.254 Chirality : 0.039 0.168 3523 Planarity : 0.004 0.041 4196 Dihedral : 3.768 23.230 3267 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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 (0.16), residues: 2879 helix: 1.78 (0.16), residues: 1035 sheet: -0.09 (0.23), residues: 525 loop : -0.43 (0.17), residues: 1319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 2.670 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 142 average time/residue: 0.4069 time to fit residues: 91.4606 Evaluate side-chains 138 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 2.820 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3760 time to fit residues: 6.5175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 261 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 chunk 251 optimal weight: 0.0070 chunk 267 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 116 optimal weight: 0.0070 chunk 210 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 chunk 253 optimal weight: 1.9990 chunk 266 optimal weight: 0.7980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 66 ASN I 520 HIS H 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 23455 Z= 0.130 Angle : 0.476 8.289 31916 Z= 0.239 Chirality : 0.038 0.152 3523 Planarity : 0.004 0.041 4196 Dihedral : 3.600 21.688 3267 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: 0.81 (0.16), residues: 2879 helix: 1.96 (0.16), residues: 1035 sheet: -0.00 (0.23), residues: 533 loop : -0.34 (0.17), residues: 1311 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 145 time to evaluate : 2.772 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 147 average time/residue: 0.4245 time to fit residues: 96.1068 Evaluate side-chains 135 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 2.639 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2087 time to fit residues: 4.2705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 3.9990 chunk 283 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 196 optimal weight: 1.9990 chunk 296 optimal weight: 20.0000 chunk 273 optimal weight: 8.9990 chunk 236 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 520 HIS H 104 ASN H 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 23455 Z= 0.189 Angle : 0.505 8.046 31916 Z= 0.254 Chirality : 0.039 0.154 3523 Planarity : 0.004 0.058 4196 Dihedral : 3.723 22.714 3267 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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 (0.16), residues: 2879 helix: 1.90 (0.16), residues: 1032 sheet: 0.03 (0.23), residues: 519 loop : -0.34 (0.17), residues: 1328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5758 Ramachandran restraints generated. 2879 Oldfield, 0 Emsley, 2879 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 2.568 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 135 average time/residue: 0.3901 time to fit residues: 84.4904 Evaluate side-chains 131 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 2.843 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2555 time to fit residues: 5.3233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 0.1980 chunk 236 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 548 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 520 HIS H 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.113958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.086915 restraints weight = 53558.219| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.43 r_work: 0.3145 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.066 23455 Z= 0.299 Angle : 0.574 8.817 31916 Z= 0.292 Chirality : 0.042 0.171 3523 Planarity : 0.004 0.053 4196 Dihedral : 4.125 27.280 3267 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.05 % 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: 0.36 (0.16), residues: 2879 helix: 1.56 (0.16), residues: 1035 sheet: -0.20 (0.23), residues: 500 loop : -0.58 (0.17), residues: 1344 =============================================================================== Job complete usr+sys time: 5615.06 seconds wall clock time: 102 minutes 38.92 seconds (6158.92 seconds total)