Starting phenix.real_space_refine on Tue Mar 19 02:40:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrj_22446/03_2024/7jrj_22446.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrj_22446/03_2024/7jrj_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_22446/03_2024/7jrj_22446.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrj_22446/03_2024/7jrj_22446.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrj_22446/03_2024/7jrj_22446.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jrj_22446/03_2024/7jrj_22446.pdb" } resolution = 3.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 12.18, per 1000 atoms: 0.53 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: 8.80 Conformation dependent library (CDL) restraints added in 4.3 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: 3.01 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: 8.31 Time building geometry restraints manager: 9.44 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: 13.510 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: 35.030 Check model and map are aligned: 0.370 Set scattering table: 0.230 Process input model: 61.180 Find NCS groups from input model: 0.860 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.170 ------------------------------------------------------------------------------- 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 % Allowed : 6.74 % Favored : 93.22 % 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: -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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 99 HIS 0.004 0.001 HIS K 121 PHE 0.016 0.001 PHE E 122 TYR 0.016 0.002 TYR D 130 ARG 0.004 0.001 ARG A 107 *********************** 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 : 2.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 102 ASP cc_start: 0.7992 (t0) cc_final: 0.7728 (t0) REVERT: F 583 ASP cc_start: 0.7235 (t0) cc_final: 0.6993 (t0) REVERT: K 45 ARG cc_start: 0.7192 (tpt-90) cc_final: 0.6966 (ttm-80) REVERT: H 108 ILE cc_start: 0.8013 (tt) cc_final: 0.7738 (mt) REVERT: C 301 ARG cc_start: 0.7105 (ttm170) cc_final: 0.6441 (tpp80) REVERT: D 58 ASN cc_start: 0.7784 (t0) cc_final: 0.7430 (m-40) REVERT: D 90 ASP cc_start: 0.7350 (t0) cc_final: 0.6945 (t0) outliers start: 1 outliers final: 1 residues processed: 313 average time/residue: 0.4078 time to fit residues: 185.3492 Evaluate side-chains 155 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 154 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 495 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 251 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 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: 0.8580 ------------------------------------------------------------------------------- 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 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1475 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= 0.170 Angle : 0.528 7.179 31916 Z= 0.271 Chirality : 0.039 0.203 3523 Planarity : 0.004 0.052 4196 Dihedral : 4.140 26.594 3268 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.01 % Allowed : 9.64 % Favored : 89.34 % 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: -0.95 (0.15), residues: 2879 helix: 0.45 (0.16), residues: 1034 sheet: -0.82 (0.23), residues: 510 loop : -1.38 (0.16), residues: 1335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 99 HIS 0.008 0.001 HIS G 507 PHE 0.014 0.001 PHE A 186 TYR 0.016 0.002 TYR B 60 ARG 0.009 0.000 ARG K 88 *********************** 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 202 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 356 THR cc_start: 0.7689 (OUTLIER) cc_final: 0.7256 (m) REVERT: G 472 ASP cc_start: 0.7608 (p0) cc_final: 0.7082 (p0) REVERT: G 480 MET cc_start: 0.7704 (mtp) cc_final: 0.7442 (ptp) REVERT: H 108 ILE cc_start: 0.8022 (tt) cc_final: 0.7769 (mt) REVERT: C 301 ARG cc_start: 0.6841 (ttm170) cc_final: 0.6438 (tpp80) REVERT: C 313 MET cc_start: 0.7515 (mtm) cc_final: 0.7157 (mtm) REVERT: D 58 ASN cc_start: 0.7747 (t0) cc_final: 0.7429 (m-40) REVERT: D 90 ASP cc_start: 0.7165 (t0) cc_final: 0.6957 (t0) REVERT: D 92 GLU cc_start: 0.7172 (pp20) cc_final: 0.6833 (pp20) outliers start: 23 outliers final: 9 residues processed: 191 average time/residue: 0.3844 time to fit residues: 111.3624 Evaluate side-chains 164 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 154 time to evaluate : 2.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 725 GLN Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain C residue 43 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 150 optimal weight: 0.0010 chunk 83 optimal weight: 0.8980 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: 0.7980 chunk 92 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN A 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1933 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= 0.227 Angle : 0.539 10.245 31916 Z= 0.273 Chirality : 0.040 0.180 3523 Planarity : 0.004 0.050 4196 Dihedral : 4.093 25.980 3267 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.67 % Allowed : 10.35 % Favored : 87.98 % 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: -0.38 (0.15), residues: 2879 helix: 0.94 (0.16), residues: 1035 sheet: -0.52 (0.23), residues: 512 loop : -1.06 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 103 HIS 0.009 0.001 HIS G 507 PHE 0.016 0.001 PHE E 122 TYR 0.017 0.002 TYR B 60 ARG 0.004 0.000 ARG B 44 *********************** 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 198 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 160 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 550 PHE cc_start: 0.6152 (m-80) cc_final: 0.5715 (m-80) REVERT: G 283 LYS cc_start: 0.8410 (mttt) cc_final: 0.8176 (mtmm) REVERT: G 356 THR cc_start: 0.7828 (OUTLIER) cc_final: 0.7512 (m) REVERT: G 472 ASP cc_start: 0.7794 (OUTLIER) cc_final: 0.7272 (p0) REVERT: H 108 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7830 (mt) REVERT: A 196 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: C 313 MET cc_start: 0.7618 (mtm) cc_final: 0.7220 (mtm) REVERT: D 58 ASN cc_start: 0.7839 (t0) cc_final: 0.7527 (m-40) REVERT: D 90 ASP cc_start: 0.7074 (t0) cc_final: 0.6833 (t0) outliers start: 38 outliers final: 17 residues processed: 187 average time/residue: 0.3869 time to fit residues: 110.9672 Evaluate side-chains 164 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain I residue 512 SER Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 332 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 267 optimal weight: 0.6980 chunk 203 optimal weight: 0.7980 chunk 140 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 129 optimal weight: 0.0370 chunk 182 optimal weight: 3.9990 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: 0.6980 overall best weight: 1.2460 ------------------------------------------------------------------------------- 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 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 518 HIS I 520 HIS D 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23455 Z= 0.188 Angle : 0.506 8.355 31916 Z= 0.256 Chirality : 0.039 0.202 3523 Planarity : 0.004 0.047 4196 Dihedral : 3.960 24.962 3267 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.72 % Allowed : 11.05 % Favored : 87.23 % 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: 0.01 (0.16), residues: 2879 helix: 1.30 (0.16), residues: 1025 sheet: -0.35 (0.23), residues: 525 loop : -0.83 (0.17), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 103 HIS 0.010 0.001 HIS G 507 PHE 0.013 0.001 PHE E 122 TYR 0.015 0.001 TYR B 60 ARG 0.005 0.000 ARG G 352 *********************** 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 194 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 550 PHE cc_start: 0.6183 (m-80) cc_final: 0.5631 (m-80) REVERT: G 283 LYS cc_start: 0.8407 (mttt) cc_final: 0.8178 (mtmm) REVERT: G 356 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7745 (m) REVERT: G 472 ASP cc_start: 0.7718 (OUTLIER) cc_final: 0.7381 (p0) REVERT: H 108 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7843 (mt) REVERT: A 196 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.6966 (mp0) REVERT: C 313 MET cc_start: 0.7671 (mtm) cc_final: 0.7244 (mtm) REVERT: D 4 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.6640 (t0) REVERT: D 58 ASN cc_start: 0.7739 (t0) cc_final: 0.7500 (m-40) REVERT: D 90 ASP cc_start: 0.7169 (t0) cc_final: 0.6965 (t0) outliers start: 39 outliers final: 19 residues processed: 185 average time/residue: 0.3611 time to fit residues: 102.9014 Evaluate side-chains 168 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 144 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain G residue 356 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain G residue 472 ASP Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 332 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 239 optimal weight: 2.9990 chunk 163 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 214 optimal weight: 2.9990 chunk 118 optimal weight: 0.0980 chunk 245 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 147 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 overall best weight: 2.2188 ------------------------------------------------------------------------------- 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 ** F 725 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7984 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23455 Z= 0.305 Angle : 0.574 7.729 31916 Z= 0.291 Chirality : 0.042 0.215 3523 Planarity : 0.005 0.078 4196 Dihedral : 4.224 26.682 3267 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.20 % Allowed : 11.67 % Favored : 86.13 % 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: -0.09 (0.16), residues: 2879 helix: 1.14 (0.16), residues: 1037 sheet: -0.40 (0.23), residues: 526 loop : -0.83 (0.17), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 103 HIS 0.010 0.002 HIS G 507 PHE 0.019 0.002 PHE E 122 TYR 0.019 0.002 TYR B 60 ARG 0.007 0.001 ARG G 352 *********************** 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 196 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 146 time to evaluate : 2.322 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 108 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7735 (tm-30) REVERT: I 193 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8301 (t) REVERT: G 283 LYS cc_start: 0.8415 (mttt) cc_final: 0.8186 (mtmm) REVERT: G 472 ASP cc_start: 0.7721 (p0) cc_final: 0.7453 (p0) REVERT: H 108 ILE cc_start: 0.8157 (OUTLIER) cc_final: 0.7933 (mt) REVERT: A 196 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: C 313 MET cc_start: 0.7713 (mtm) cc_final: 0.7297 (mtm) REVERT: D 4 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.6595 (t0) REVERT: D 90 ASP cc_start: 0.7145 (t0) cc_final: 0.6918 (t0) outliers start: 50 outliers final: 27 residues processed: 185 average time/residue: 0.3540 time to fit residues: 102.4028 Evaluate side-chains 168 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 2.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 4 ASP Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 383 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 96 optimal weight: 10.0000 chunk 259 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 169 optimal weight: 0.0670 chunk 71 optimal weight: 10.0000 chunk 288 optimal weight: 20.0000 chunk 239 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 151 optimal weight: 0.0370 overall best weight: 0.7998 ------------------------------------------------------------------------------- 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 725 GLN I 520 HIS H 104 ASN H 477 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23455 Z= 0.151 Angle : 0.491 7.249 31916 Z= 0.248 Chirality : 0.039 0.197 3523 Planarity : 0.004 0.043 4196 Dihedral : 3.894 23.827 3267 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.50 % Allowed : 12.90 % Favored : 85.60 % 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: 0.33 (0.16), residues: 2879 helix: 1.56 (0.16), residues: 1029 sheet: -0.23 (0.23), residues: 529 loop : -0.62 (0.17), residues: 1321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP H 103 HIS 0.004 0.001 HIS I 495 PHE 0.011 0.001 PHE B 242 TYR 0.013 0.001 TYR B 60 ARG 0.005 0.000 ARG G 352 *********************** 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 181 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 2.554 Fit side-chains revert: symmetry clash REVERT: I 193 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8207 (t) REVERT: G 283 LYS cc_start: 0.8418 (mttt) cc_final: 0.8186 (mtmm) REVERT: A 196 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: C 313 MET cc_start: 0.7624 (mtm) cc_final: 0.7204 (mtm) REVERT: D 90 ASP cc_start: 0.7129 (t0) cc_final: 0.6896 (t0) REVERT: D 92 GLU cc_start: 0.7088 (pp20) cc_final: 0.6767 (pp20) outliers start: 34 outliers final: 21 residues processed: 173 average time/residue: 0.3699 time to fit residues: 99.0523 Evaluate side-chains 159 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 2.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain H residue 477 GLN Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 383 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 277 optimal weight: 0.9990 chunk 32 optimal weight: 10.0000 chunk 164 optimal weight: 0.5980 chunk 210 optimal weight: 4.9990 chunk 163 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 725 GLN I 520 HIS H 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 23455 Z= 0.261 Angle : 0.540 8.311 31916 Z= 0.273 Chirality : 0.041 0.220 3523 Planarity : 0.004 0.045 4196 Dihedral : 4.032 25.036 3267 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.67 % Allowed : 12.95 % Favored : 85.38 % 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: 0.26 (0.16), residues: 2879 helix: 1.48 (0.16), residues: 1030 sheet: -0.22 (0.23), residues: 523 loop : -0.67 (0.17), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 103 HIS 0.007 0.001 HIS A 32 PHE 0.016 0.001 PHE E 122 TYR 0.018 0.002 TYR B 60 ARG 0.009 0.000 ARG K 160 *********************** 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 179 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 141 time to evaluate : 2.462 Fit side-chains REVERT: F 459 ASP cc_start: 0.7426 (p0) cc_final: 0.7156 (p0) REVERT: I 108 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7728 (tm-30) REVERT: I 193 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8310 (t) REVERT: G 283 LYS cc_start: 0.8432 (mttt) cc_final: 0.8193 (mtmm) REVERT: A 196 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7164 (mp0) REVERT: C 313 MET cc_start: 0.7616 (mtm) cc_final: 0.7227 (mtm) REVERT: D 12 LEU cc_start: 0.8101 (tp) cc_final: 0.7214 (mt) REVERT: D 90 ASP cc_start: 0.7138 (t0) cc_final: 0.6907 (t0) REVERT: D 92 GLU cc_start: 0.7072 (pp20) cc_final: 0.6758 (pp20) outliers start: 38 outliers final: 29 residues processed: 174 average time/residue: 0.3774 time to fit residues: 101.8705 Evaluate side-chains 166 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 725 GLN Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 383 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 177 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 171 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 225 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 725 GLN K 66 ASN I 520 HIS H 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2773 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= 0.167 Angle : 0.497 8.085 31916 Z= 0.251 Chirality : 0.039 0.171 3523 Planarity : 0.004 0.057 4196 Dihedral : 3.874 24.008 3267 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.45 % Allowed : 13.39 % Favored : 85.16 % 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: 0.48 (0.16), residues: 2879 helix: 1.71 (0.16), residues: 1029 sheet: -0.17 (0.23), residues: 527 loop : -0.54 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 103 HIS 0.003 0.001 HIS A 32 PHE 0.011 0.001 PHE E 122 TYR 0.014 0.001 TYR B 60 ARG 0.007 0.000 ARG K 160 *********************** 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 172 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 2.684 Fit side-chains REVERT: I 193 VAL cc_start: 0.8475 (OUTLIER) cc_final: 0.8226 (t) REVERT: G 283 LYS cc_start: 0.8421 (mttt) cc_final: 0.8174 (mtmm) REVERT: A 196 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7219 (mp0) REVERT: C 313 MET cc_start: 0.7595 (mtm) cc_final: 0.7224 (mtm) REVERT: D 12 LEU cc_start: 0.8037 (tp) cc_final: 0.7210 (mt) REVERT: D 90 ASP cc_start: 0.7181 (t0) cc_final: 0.6942 (t0) outliers start: 33 outliers final: 25 residues processed: 167 average time/residue: 0.3574 time to fit residues: 93.4055 Evaluate side-chains 161 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 2.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 363 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 472 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 383 VAL 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: 3.9990 chunk 251 optimal weight: 7.9990 chunk 267 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 210 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 266 optimal weight: 0.9980 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 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 : 0.005 0.070 23455 Z= 0.312 Angle : 0.574 8.583 31916 Z= 0.292 Chirality : 0.042 0.188 3523 Planarity : 0.005 0.058 4196 Dihedral : 4.162 26.235 3267 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.76 % Allowed : 13.08 % Favored : 85.16 % 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: 0.21 (0.16), residues: 2879 helix: 1.47 (0.16), residues: 1026 sheet: -0.30 (0.23), residues: 500 loop : -0.69 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 103 HIS 0.007 0.001 HIS A 32 PHE 0.019 0.002 PHE E 122 TYR 0.020 0.002 TYR B 60 ARG 0.009 0.001 ARG K 160 *********************** 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 178 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 138 time to evaluate : 2.652 Fit side-chains REVERT: I 108 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7708 (tm-30) REVERT: I 193 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8329 (t) REVERT: G 283 LYS cc_start: 0.8443 (mttt) cc_final: 0.8206 (mtmm) REVERT: A 196 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7165 (mp0) REVERT: C 313 MET cc_start: 0.7698 (mtm) cc_final: 0.7307 (mtm) outliers start: 40 outliers final: 31 residues processed: 171 average time/residue: 0.3622 time to fit residues: 97.6821 Evaluate side-chains 165 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 132 time to evaluate : 2.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 84 LYS Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 539 LEU Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 683 THR Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain H residue 240 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 175 optimal weight: 0.7980 chunk 283 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 134 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 296 optimal weight: 20.0000 chunk 273 optimal weight: 9.9990 chunk 236 optimal weight: 0.0060 chunk 24 optimal weight: 0.0000 chunk 182 optimal weight: 3.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- 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 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 520 HIS H 104 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 23455 Z= 0.160 Angle : 0.501 8.677 31916 Z= 0.252 Chirality : 0.039 0.173 3523 Planarity : 0.004 0.043 4196 Dihedral : 3.894 24.368 3267 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.32 % Allowed : 13.43 % Favored : 85.25 % 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: 0.51 (0.16), residues: 2879 helix: 1.76 (0.16), residues: 1025 sheet: -0.18 (0.23), residues: 500 loop : -0.53 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 49 HIS 0.003 0.001 HIS K 55 PHE 0.011 0.001 PHE A 242 TYR 0.014 0.001 TYR B 60 ARG 0.010 0.000 ARG G 352 ********************** 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 166 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 2.752 Fit side-chains REVERT: I 108 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7659 (tm-30) REVERT: I 193 VAL cc_start: 0.8493 (OUTLIER) cc_final: 0.8249 (t) REVERT: A 196 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: C 313 MET cc_start: 0.7623 (mtm) cc_final: 0.7265 (mtm) REVERT: D 12 LEU cc_start: 0.8014 (tp) cc_final: 0.7029 (mt) outliers start: 30 outliers final: 24 residues processed: 160 average time/residue: 0.3601 time to fit residues: 90.6572 Evaluate side-chains 159 residues out of total 2281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 2.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 ASP Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 162 SER Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain F residue 473 VAL Chi-restraints excluded: chain F residue 642 ASP Chi-restraints excluded: chain F residue 664 THR Chi-restraints excluded: chain F residue 740 ILE Chi-restraints excluded: chain F residue 770 LYS Chi-restraints excluded: chain K residue 131 ARG Chi-restraints excluded: chain K residue 139 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 193 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain H residue 104 ASN Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain B residue 92 SER Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 416 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 298 random chunks: chunk 187 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 217 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 43 optimal weight: 6.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 520 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.104949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.078514 restraints weight = 52787.688| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.47 r_work: 0.3158 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.196 23455 Z= 0.270 Angle : 0.674 59.194 31916 Z= 0.383 Chirality : 0.041 0.471 3523 Planarity : 0.004 0.043 4196 Dihedral : 3.905 24.483 3267 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.19 % Allowed : 13.74 % Favored : 85.07 % Cbeta Deviations : 0.04 % 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: 0.49 (0.16), residues: 2879 helix: 1.73 (0.16), residues: 1025 sheet: -0.18 (0.23), residues: 500 loop : -0.53 (0.17), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 99 HIS 0.003 0.001 HIS B 14 PHE 0.012 0.001 PHE E 122 TYR 0.015 0.002 TYR B 60 ARG 0.009 0.000 ARG G 352 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6304.75 seconds wall clock time: 113 minutes 40.98 seconds (6820.98 seconds total)