Starting phenix.real_space_refine on Thu Feb 22 07:30:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fne_29310/02_2024/8fne_29310.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fne_29310/02_2024/8fne_29310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fne_29310/02_2024/8fne_29310.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fne_29310/02_2024/8fne_29310.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fne_29310/02_2024/8fne_29310.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fne_29310/02_2024/8fne_29310.pdb" } resolution = 3.9 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= 2.062 sd= 0.266 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 10620 2.51 5 N 2964 2.21 5 O 3212 1.98 5 H 16644 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 104": "OD1" <-> "OD2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 170": "OD1" <-> "OD2" Residue "A ARG 195": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 370": "OD1" <-> "OD2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 71": "OD1" <-> "OD2" Residue "B ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 344": "OD1" <-> "OD2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 71": "OD1" <-> "OD2" Residue "C ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 134": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 344": "OD1" <-> "OD2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 378": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 62": "OD1" <-> "OD2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 104": "OD1" <-> "OD2" Residue "D TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "D ARG 195": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 198": "OE1" <-> "OE2" Residue "D TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 302": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 333": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ASP 370": "OD1" <-> "OD2" Residue "D PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 436": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 509": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 513": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 601": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 602": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33508 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 8213 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 21, 'TRANS': 503} Chain breaks: 1 Chain: "B" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 8213 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 21, 'TRANS': 503} Chain breaks: 1 Chain: "C" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 8213 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 21, 'TRANS': 503} Chain breaks: 1 Chain: "D" Number of atoms: 8213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 8213 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 21, 'TRANS': 503} Chain breaks: 1 Chain: "E" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 164 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "F" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 164 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "G" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 164 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Chain: "H" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 164 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 15.77, per 1000 atoms: 0.47 Number of scatterers: 33508 At special positions: 0 Unit cell: (157.626, 157.626, 75.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 O 3212 8.00 N 2964 7.00 C 10620 6.00 H 16644 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 28.99 Conformation dependent library (CDL) restraints added in 3.9 seconds 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3992 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 24 sheets defined 41.6% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.51 Creating SS restraints... Processing helix chain 'A' and resid 19 through 21 No H-bonds generated for 'chain 'A' and resid 19 through 21' Processing helix chain 'A' and resid 22 through 27 Processing helix chain 'A' and resid 36 through 56 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 135 through 151 Processing helix chain 'A' and resid 173 through 196 Processing helix chain 'A' and resid 202 through 207 removed outlier: 3.513A pdb=" N LEU A 206 " --> pdb=" O SER A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 328 removed outlier: 3.939A pdb=" N SER A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASN A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR A 326 " --> pdb=" O ALA A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 336 removed outlier: 3.509A pdb=" N ARG A 333 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 Processing helix chain 'A' and resid 369 through 381 Processing helix chain 'A' and resid 397 through 407 removed outlier: 4.496A pdb=" N VAL A 403 " --> pdb=" O ALA A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 429 Processing helix chain 'A' and resid 431 through 435 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 470 through 478 Processing helix chain 'A' and resid 481 through 492 Processing helix chain 'A' and resid 498 through 514 Processing helix chain 'A' and resid 530 through 543 Processing helix chain 'B' and resid 20 through 27 removed outlier: 5.115A pdb=" N ILE B 25 " --> pdb=" O ASN B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 56 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 135 through 151 Processing helix chain 'B' and resid 173 through 196 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 311 through 324 removed outlier: 3.833A pdb=" N SER B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA B 322 " --> pdb=" O ALA B 318 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 329 through 336 Processing helix chain 'B' and resid 347 through 354 Processing helix chain 'B' and resid 369 through 381 Processing helix chain 'B' and resid 397 through 407 removed outlier: 4.222A pdb=" N VAL B 403 " --> pdb=" O ALA B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 429 Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 470 through 478 Processing helix chain 'B' and resid 481 through 492 removed outlier: 3.956A pdb=" N GLN B 492 " --> pdb=" O TRP B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 530 through 543 Processing helix chain 'C' and resid 20 through 27 removed outlier: 5.116A pdb=" N ILE C 25 " --> pdb=" O ASN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 56 Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 129 through 134 Processing helix chain 'C' and resid 135 through 151 Processing helix chain 'C' and resid 173 through 196 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 311 through 324 removed outlier: 3.833A pdb=" N SER C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASN C 321 " --> pdb=" O PHE C 317 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA C 322 " --> pdb=" O ALA C 318 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 329 through 336 Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 369 through 381 Processing helix chain 'C' and resid 397 through 407 removed outlier: 4.222A pdb=" N VAL C 403 " --> pdb=" O ALA C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 429 Processing helix chain 'C' and resid 431 through 435 Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 470 through 478 Processing helix chain 'C' and resid 481 through 492 removed outlier: 3.955A pdb=" N GLN C 492 " --> pdb=" O TRP C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 515 Processing helix chain 'C' and resid 530 through 543 Processing helix chain 'D' and resid 19 through 21 No H-bonds generated for 'chain 'D' and resid 19 through 21' Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 36 through 56 Processing helix chain 'D' and resid 129 through 134 Processing helix chain 'D' and resid 135 through 151 Processing helix chain 'D' and resid 173 through 196 Processing helix chain 'D' and resid 202 through 207 removed outlier: 3.512A pdb=" N LEU D 206 " --> pdb=" O SER D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 328 removed outlier: 3.940A pdb=" N SER D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ASN D 321 " --> pdb=" O PHE D 317 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL D 325 " --> pdb=" O ASN D 321 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR D 326 " --> pdb=" O ALA D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 336 removed outlier: 3.509A pdb=" N ARG D 333 " --> pdb=" O SER D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 347 through 354 Processing helix chain 'D' and resid 369 through 381 Processing helix chain 'D' and resid 397 through 407 removed outlier: 4.495A pdb=" N VAL D 403 " --> pdb=" O ALA D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 429 Processing helix chain 'D' and resid 431 through 435 Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 470 through 478 Processing helix chain 'D' and resid 481 through 492 Processing helix chain 'D' and resid 498 through 514 Processing helix chain 'D' and resid 530 through 543 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 68 removed outlier: 6.524A pdb=" N GLN A 92 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE A 158 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 94 " --> pdb=" O ILE A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 68 Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 117 Processing sheet with id=AA4, first strand: chain 'A' and resid 444 through 446 removed outlier: 6.904A pdb=" N VAL A 518 " --> pdb=" O LEU A 457 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU A 457 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR A 520 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR A 455 " --> pdb=" O TYR A 520 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR A 522 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU A 453 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 446 removed outlier: 5.480A pdb=" N PHE A 387 " --> pdb=" O TRP A 529 " (cutoff:3.500A) removed outlier: 8.898A pdb=" N VAL A 386 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N MET A 388 " --> pdb=" O PRO A 294 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE A 296 " --> pdb=" O MET A 388 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP A 390 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE A 298 " --> pdb=" O ASP A 390 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER A 264 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL A 301 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN A 262 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLN A 303 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 260 " --> pdb=" O GLN A 303 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N LEU A 240 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 262 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 238 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N SER A 264 " --> pdb=" O ILE A 236 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE A 236 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ALA A 214 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU A 213 " --> pdb=" O ALA A 549 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 224 through 225 removed outlier: 3.769A pdb=" N MET A 224 " --> pdb=" O ILE A 232 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 68 removed outlier: 4.137A pdb=" N SER B 78 " --> pdb=" O MET B 101 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 64 through 68 removed outlier: 4.137A pdb=" N SER B 78 " --> pdb=" O MET B 101 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 110 through 117 Processing sheet with id=AB1, first strand: chain 'B' and resid 444 through 446 removed outlier: 6.101A pdb=" N VAL B 518 " --> pdb=" O LEU B 457 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B 457 " --> pdb=" O VAL B 518 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR B 520 " --> pdb=" O TYR B 455 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N TYR B 455 " --> pdb=" O TYR B 520 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 522 " --> pdb=" O LEU B 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 444 through 446 removed outlier: 5.362A pdb=" N PHE B 387 " --> pdb=" O TRP B 529 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N VAL B 386 " --> pdb=" O LEU B 292 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N MET B 388 " --> pdb=" O PRO B 294 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE B 296 " --> pdb=" O MET B 388 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ASP B 390 " --> pdb=" O ILE B 296 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE B 298 " --> pdb=" O ASP B 390 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER B 264 " --> pdb=" O THR B 299 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL B 301 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN B 262 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLN B 303 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU B 260 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU B 240 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN B 262 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 238 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER B 264 " --> pdb=" O ILE B 236 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE B 236 " --> pdb=" O SER B 264 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ALA B 549 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N LEU B 213 " --> pdb=" O ALA B 549 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 225 Processing sheet with id=AB4, first strand: chain 'C' and resid 64 through 68 removed outlier: 4.137A pdb=" N SER C 78 " --> pdb=" O MET C 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 64 through 68 removed outlier: 4.137A pdb=" N SER C 78 " --> pdb=" O MET C 101 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 110 through 117 Processing sheet with id=AB7, first strand: chain 'C' and resid 444 through 446 removed outlier: 6.101A pdb=" N VAL C 518 " --> pdb=" O LEU C 457 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU C 457 " --> pdb=" O VAL C 518 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR C 520 " --> pdb=" O TYR C 455 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N TYR C 455 " --> pdb=" O TYR C 520 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR C 522 " --> pdb=" O LEU C 453 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 444 through 446 removed outlier: 5.362A pdb=" N PHE C 387 " --> pdb=" O TRP C 529 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N VAL C 386 " --> pdb=" O LEU C 292 " (cutoff:3.500A) removed outlier: 7.945A pdb=" N MET C 388 " --> pdb=" O PRO C 294 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE C 296 " --> pdb=" O MET C 388 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASP C 390 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE C 298 " --> pdb=" O ASP C 390 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N SER C 264 " --> pdb=" O THR C 299 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL C 301 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N GLN C 262 " --> pdb=" O VAL C 301 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLN C 303 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LEU C 260 " --> pdb=" O GLN C 303 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LEU C 240 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN C 262 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 238 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER C 264 " --> pdb=" O ILE C 236 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE C 236 " --> pdb=" O SER C 264 " (cutoff:3.500A) removed outlier: 9.540A pdb=" N ALA C 549 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU C 213 " --> pdb=" O ALA C 549 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 224 through 225 Processing sheet with id=AC1, first strand: chain 'D' and resid 64 through 68 removed outlier: 6.524A pdb=" N GLN D 92 " --> pdb=" O MET D 156 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N ILE D 158 " --> pdb=" O GLN D 92 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE D 94 " --> pdb=" O ILE D 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 64 through 68 Processing sheet with id=AC3, first strand: chain 'D' and resid 111 through 117 Processing sheet with id=AC4, first strand: chain 'D' and resid 444 through 446 removed outlier: 6.904A pdb=" N VAL D 518 " --> pdb=" O LEU D 457 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N LEU D 457 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N TYR D 520 " --> pdb=" O TYR D 455 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TYR D 455 " --> pdb=" O TYR D 520 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N THR D 522 " --> pdb=" O LEU D 453 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU D 453 " --> pdb=" O THR D 522 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 444 through 446 removed outlier: 5.481A pdb=" N PHE D 387 " --> pdb=" O TRP D 529 " (cutoff:3.500A) removed outlier: 8.899A pdb=" N VAL D 386 " --> pdb=" O LEU D 292 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N MET D 388 " --> pdb=" O PRO D 294 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE D 296 " --> pdb=" O MET D 388 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ASP D 390 " --> pdb=" O ILE D 296 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE D 298 " --> pdb=" O ASP D 390 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N SER D 264 " --> pdb=" O THR D 299 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N VAL D 301 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN D 262 " --> pdb=" O VAL D 301 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N GLN D 303 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU D 260 " --> pdb=" O GLN D 303 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU D 240 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN D 262 " --> pdb=" O VAL D 238 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL D 238 " --> pdb=" O GLN D 262 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N SER D 264 " --> pdb=" O ILE D 236 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ILE D 236 " --> pdb=" O SER D 264 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA D 214 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LEU D 213 " --> pdb=" O ALA D 549 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 224 through 225 removed outlier: 3.768A pdb=" N MET D 224 " --> pdb=" O ILE D 232 " (cutoff:3.500A) 864 hydrogen bonds defined for protein. 2316 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: 14.01 Time building geometry restraints manager: 29.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.70 - 0.93: 8 0.93 - 1.15: 16620 1.15 - 1.38: 6436 1.38 - 1.60: 10634 1.60 - 1.82: 122 Bond restraints: 33820 Sorted by residual: bond pdb=" NE2 HIS D 120 " pdb=" HE2 HIS D 120 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.66e+01 bond pdb=" NE2 HIS A 120 " pdb=" HE2 HIS A 120 " ideal model delta sigma weight residual 0.860 1.046 -0.186 2.00e-02 2.50e+03 8.62e+01 bond pdb=" NE2 GLN A 288 " pdb="HE22 GLN A 288 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.42e+01 bond pdb=" NE2 GLN D 288 " pdb="HE22 GLN D 288 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.34e+01 bond pdb=" NH2 ARG D 382 " pdb="HH22 ARG D 382 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.82e+01 ... (remaining 33815 not shown) Histogram of bond angle deviations from ideal: 65.84 - 79.54: 4 79.54 - 93.23: 2 93.23 - 106.93: 2513 106.93 - 120.62: 50920 120.62 - 134.32: 7577 Bond angle restraints: 61016 Sorted by residual: angle pdb=" N TYR C 513 " pdb=" CA TYR C 513 " pdb=" HA TYR C 513 " ideal model delta sigma weight residual 110.00 65.84 44.16 3.00e+00 1.11e-01 2.17e+02 angle pdb=" N TYR B 513 " pdb=" CA TYR B 513 " pdb=" HA TYR B 513 " ideal model delta sigma weight residual 110.00 65.87 44.13 3.00e+00 1.11e-01 2.16e+02 angle pdb=" CB TYR C 513 " pdb=" CA TYR C 513 " pdb=" HA TYR C 513 " ideal model delta sigma weight residual 109.00 77.78 31.22 3.00e+00 1.11e-01 1.08e+02 angle pdb=" CB TYR B 513 " pdb=" CA TYR B 513 " pdb=" HA TYR B 513 " ideal model delta sigma weight residual 109.00 77.81 31.19 3.00e+00 1.11e-01 1.08e+02 angle pdb=" C TYR B 513 " pdb=" CA TYR B 513 " pdb=" HA TYR B 513 " ideal model delta sigma weight residual 109.00 83.17 25.83 3.00e+00 1.11e-01 7.41e+01 ... (remaining 61011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 14928 16.91 - 33.81: 658 33.81 - 50.72: 172 50.72 - 67.62: 114 67.62 - 84.53: 16 Dihedral angle restraints: 15888 sinusoidal: 8732 harmonic: 7156 Sorted by residual: dihedral pdb=" CA SER B 543 " pdb=" C SER B 543 " pdb=" N VAL B 544 " pdb=" CA VAL B 544 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ALA D 167 " pdb=" C ALA D 167 " pdb=" N ASP D 168 " pdb=" CA ASP D 168 " ideal model delta harmonic sigma weight residual 180.00 -151.57 -28.43 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA SER C 543 " pdb=" C SER C 543 " pdb=" N VAL C 544 " pdb=" CA VAL C 544 " ideal model delta harmonic sigma weight residual 180.00 151.58 28.42 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 15885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1692 0.088 - 0.175: 693 0.175 - 0.263: 162 0.263 - 0.350: 31 0.350 - 0.438: 6 Chirality restraints: 2584 Sorted by residual: chirality pdb=" CB ILE A 158 " pdb=" CA ILE A 158 " pdb=" CG1 ILE A 158 " pdb=" CG2 ILE A 158 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CB ILE D 158 " pdb=" CA ILE D 158 " pdb=" CG1 ILE D 158 " pdb=" CG2 ILE D 158 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA ALA B 554 " pdb=" N ALA B 554 " pdb=" C ALA B 554 " pdb=" CB ALA B 554 " both_signs ideal model delta sigma weight residual False 2.48 2.05 0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 2581 not shown) Planarity restraints: 5140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 38 " -0.086 9.50e-02 1.11e+02 8.92e-02 1.61e+02 pdb=" NE ARG A 38 " 0.044 2.00e-02 2.50e+03 pdb=" CZ ARG A 38 " 0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG A 38 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG A 38 " 0.124 2.00e-02 2.50e+03 pdb="HH11 ARG A 38 " -0.038 2.00e-02 2.50e+03 pdb="HH12 ARG A 38 " -0.073 2.00e-02 2.50e+03 pdb="HH21 ARG A 38 " -0.183 2.00e-02 2.50e+03 pdb="HH22 ARG A 38 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 38 " 0.086 9.50e-02 1.11e+02 8.92e-02 1.61e+02 pdb=" NE ARG D 38 " -0.044 2.00e-02 2.50e+03 pdb=" CZ ARG D 38 " -0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG D 38 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG D 38 " -0.123 2.00e-02 2.50e+03 pdb="HH11 ARG D 38 " 0.038 2.00e-02 2.50e+03 pdb="HH12 ARG D 38 " 0.073 2.00e-02 2.50e+03 pdb="HH21 ARG D 38 " 0.183 2.00e-02 2.50e+03 pdb="HH22 ARG D 38 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 317 " 0.154 2.00e-02 2.50e+03 5.90e-02 1.04e+02 pdb=" CG PHE D 317 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE D 317 " -0.052 2.00e-02 2.50e+03 pdb=" CD2 PHE D 317 " -0.043 2.00e-02 2.50e+03 pdb=" CE1 PHE D 317 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 PHE D 317 " -0.014 2.00e-02 2.50e+03 pdb=" CZ PHE D 317 " 0.019 2.00e-02 2.50e+03 pdb=" HD1 PHE D 317 " -0.047 2.00e-02 2.50e+03 pdb=" HD2 PHE D 317 " -0.050 2.00e-02 2.50e+03 pdb=" HE1 PHE D 317 " 0.006 2.00e-02 2.50e+03 pdb=" HE2 PHE D 317 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE D 317 " 0.082 2.00e-02 2.50e+03 ... (remaining 5137 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 1441 2.09 - 2.72: 52528 2.72 - 3.34: 99939 3.34 - 3.97: 130828 3.97 - 4.60: 194137 Nonbonded interactions: 478873 Sorted by model distance: nonbonded pdb=" HE2 MET A 205 " pdb="HD23 LEU C 22 " model vdw 1.461 2.440 nonbonded pdb="HD23 LEU B 22 " pdb=" HE2 MET D 205 " model vdw 1.462 2.440 nonbonded pdb=" H THR A 440 " pdb=" H MET A 441 " model vdw 1.492 2.100 nonbonded pdb=" H THR D 440 " pdb=" H MET D 441 " model vdw 1.492 2.100 nonbonded pdb=" OD1 ASP A 190 " pdb=" HG SER C 29 " model vdw 1.588 1.850 ... (remaining 478868 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.790 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: 0.500 Extract box with map and model: 29.430 Check model and map are aligned: 0.540 Set scattering table: 0.320 Process input model: 111.750 Find NCS groups from input model: 1.560 Set up NCS constraints: 0.180 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: 0.000 Load rotamer database and sin/cos tables:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4678 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 : 0.018 0.107 17176 Z= 1.167 Angle : 1.776 12.129 23268 Z= 1.215 Chirality : 0.099 0.438 2584 Planarity : 0.010 0.091 3088 Dihedral : 11.330 84.528 6364 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 0.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2124 helix: -0.44 (0.17), residues: 740 sheet: 0.80 (0.24), residues: 466 loop : 0.70 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.010 TRP C 139 HIS 0.010 0.002 HIS D 60 PHE 0.090 0.010 PHE D 317 TYR 0.108 0.016 TYR G 602 ARG 0.008 0.001 ARG D 324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 810 time to evaluate : 2.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.6632 (mm) cc_final: 0.6326 (mm) REVERT: C 550 MET cc_start: 0.5411 (pmm) cc_final: 0.5170 (pmm) REVERT: D 142 ILE cc_start: 0.6524 (mm) cc_final: 0.6214 (mm) REVERT: D 297 VAL cc_start: 0.5429 (t) cc_final: 0.5181 (t) REVERT: D 451 ILE cc_start: 0.6388 (mt) cc_final: 0.6179 (mm) outliers start: 0 outliers final: 0 residues processed: 810 average time/residue: 0.7935 time to fit residues: 898.1630 Evaluate side-chains 587 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 587 time to evaluate : 2.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 GLN B 72 GLN B 505 GLN C 72 GLN C 505 GLN ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 GLN D 445 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4914 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17176 Z= 0.209 Angle : 0.648 6.067 23268 Z= 0.360 Chirality : 0.045 0.386 2584 Planarity : 0.005 0.059 3088 Dihedral : 5.429 27.641 2316 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.83 % Allowed : 12.47 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.18), residues: 2124 helix: 0.75 (0.18), residues: 726 sheet: 0.13 (0.23), residues: 436 loop : 0.72 (0.21), residues: 962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 331 HIS 0.007 0.001 HIS D 498 PHE 0.032 0.002 PHE D 373 TYR 0.017 0.002 TYR C 315 ARG 0.006 0.001 ARG B 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 636 time to evaluate : 2.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.6961 (mm-40) cc_final: 0.6394 (mm-40) REVERT: A 504 ARG cc_start: 0.4112 (ttm-80) cc_final: 0.3783 (ttm-80) REVERT: C 185 VAL cc_start: 0.6922 (t) cc_final: 0.6712 (t) REVERT: D 33 ASP cc_start: 0.6209 (p0) cc_final: 0.5900 (p0) REVERT: D 56 GLN cc_start: 0.6958 (mm110) cc_final: 0.6686 (mm110) REVERT: E 602 TYR cc_start: 0.5563 (OUTLIER) cc_final: 0.5317 (p90) outliers start: 33 outliers final: 25 residues processed: 651 average time/residue: 0.7393 time to fit residues: 698.3075 Evaluate side-chains 572 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 546 time to evaluate : 2.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 312 MET Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 501 LEU Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 347 ASP Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 85 ARG Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 548 VAL Chi-restraints excluded: chain E residue 602 TYR Chi-restraints excluded: chain G residue 602 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 208 optimal weight: 5.9990 chunk 171 optimal weight: 0.3980 chunk 191 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 GLN A 251 ASN B 73 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 397 ASN ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 HIS D 492 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5162 moved from start: 0.5778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 17176 Z= 0.240 Angle : 0.607 5.024 23268 Z= 0.336 Chirality : 0.043 0.383 2584 Planarity : 0.005 0.062 3088 Dihedral : 5.050 24.003 2316 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.83 % Allowed : 16.63 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2124 helix: 0.48 (0.18), residues: 746 sheet: -0.01 (0.23), residues: 462 loop : 0.42 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 331 HIS 0.006 0.002 HIS D 498 PHE 0.026 0.002 PHE B 533 TYR 0.017 0.002 TYR A 271 ARG 0.007 0.001 ARG B 195 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 596 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASP cc_start: 0.6272 (p0) cc_final: 0.5917 (p0) REVERT: C 213 LEU cc_start: 0.6564 (OUTLIER) cc_final: 0.6135 (mm) REVERT: D 33 ASP cc_start: 0.6474 (p0) cc_final: 0.6052 (p0) REVERT: D 314 LEU cc_start: 0.7635 (mt) cc_final: 0.7386 (mt) REVERT: E 602 TYR cc_start: 0.5719 (OUTLIER) cc_final: 0.5356 (p90) outliers start: 51 outliers final: 39 residues processed: 615 average time/residue: 0.7194 time to fit residues: 642.0707 Evaluate side-chains 585 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 544 time to evaluate : 2.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 249 GLN Chi-restraints excluded: chain A residue 251 ASN Chi-restraints excluded: chain A residue 373 PHE Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain E residue 602 TYR Chi-restraints excluded: chain F residue 602 TYR Chi-restraints excluded: chain G residue 602 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 GLN ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 GLN D 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5333 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 17176 Z= 0.285 Angle : 0.601 4.926 23268 Z= 0.337 Chirality : 0.042 0.383 2584 Planarity : 0.005 0.067 3088 Dihedral : 5.087 23.096 2316 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.49 % Allowed : 19.18 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2124 helix: 0.16 (0.18), residues: 772 sheet: -0.28 (0.23), residues: 464 loop : 0.03 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 331 HIS 0.007 0.002 HIS A 153 PHE 0.022 0.002 PHE A 533 TYR 0.013 0.002 TYR B 520 ARG 0.010 0.001 ARG C 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 559 time to evaluate : 3.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 VAL cc_start: 0.7521 (m) cc_final: 0.6875 (m) REVERT: B 49 LEU cc_start: 0.7142 (mt) cc_final: 0.6409 (mt) REVERT: B 453 LEU cc_start: 0.4769 (mp) cc_final: 0.3378 (mp) REVERT: D 33 ASP cc_start: 0.6615 (p0) cc_final: 0.6194 (p0) REVERT: D 314 LEU cc_start: 0.7717 (mt) cc_final: 0.7456 (mt) REVERT: E 602 TYR cc_start: 0.5870 (OUTLIER) cc_final: 0.5509 (p90) outliers start: 63 outliers final: 53 residues processed: 585 average time/residue: 0.7157 time to fit residues: 612.2904 Evaluate side-chains 590 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 536 time to evaluate : 2.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 253 PHE Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 334 SER Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain E residue 602 TYR Chi-restraints excluded: chain G residue 602 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 152 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5385 moved from start: 0.7487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 17176 Z= 0.256 Angle : 0.584 4.937 23268 Z= 0.323 Chirality : 0.042 0.376 2584 Planarity : 0.005 0.068 3088 Dihedral : 4.972 21.783 2316 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.16 % Allowed : 19.68 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 2124 helix: 0.16 (0.18), residues: 772 sheet: -0.51 (0.22), residues: 466 loop : -0.11 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 331 HIS 0.006 0.002 HIS A 153 PHE 0.017 0.002 PHE D 373 TYR 0.020 0.002 TYR D 455 ARG 0.009 0.001 ARG C 195 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 559 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 33 ASP cc_start: 0.6599 (p0) cc_final: 0.6376 (p0) REVERT: E 602 TYR cc_start: 0.5895 (OUTLIER) cc_final: 0.5500 (p90) outliers start: 75 outliers final: 65 residues processed: 588 average time/residue: 0.7128 time to fit residues: 616.8970 Evaluate side-chains 601 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 535 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 451 ILE Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain E residue 602 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 92 GLN B 262 GLN ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 92 GLN ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5401 moved from start: 0.8006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 17176 Z= 0.229 Angle : 0.566 5.324 23268 Z= 0.310 Chirality : 0.042 0.384 2584 Planarity : 0.005 0.073 3088 Dihedral : 4.804 20.342 2316 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.94 % Allowed : 21.51 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2124 helix: 0.30 (0.18), residues: 772 sheet: -0.51 (0.22), residues: 448 loop : -0.20 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 331 HIS 0.006 0.001 HIS D 498 PHE 0.016 0.002 PHE D 373 TYR 0.012 0.001 TYR B 456 ARG 0.009 0.001 ARG C 195 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 557 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 GLU cc_start: 0.2565 (tp30) cc_final: 0.2031 (tp30) REVERT: E 602 TYR cc_start: 0.5939 (OUTLIER) cc_final: 0.5533 (p90) outliers start: 71 outliers final: 63 residues processed: 583 average time/residue: 0.7378 time to fit residues: 627.5130 Evaluate side-chains 591 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 527 time to evaluate : 2.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ASP Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain E residue 602 TYR Chi-restraints excluded: chain F residue 602 TYR Chi-restraints excluded: chain G residue 602 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 chunk 127 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 GLN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5548 moved from start: 0.8617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 17176 Z= 0.334 Angle : 0.631 5.258 23268 Z= 0.356 Chirality : 0.042 0.378 2584 Planarity : 0.005 0.088 3088 Dihedral : 5.115 20.230 2316 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 4.93 % Allowed : 22.06 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.17), residues: 2124 helix: -0.11 (0.18), residues: 772 sheet: -0.89 (0.22), residues: 446 loop : -0.55 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 331 HIS 0.008 0.002 HIS B 498 PHE 0.018 0.002 PHE D 134 TYR 0.014 0.002 TYR D 271 ARG 0.013 0.001 ARG C 195 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 525 time to evaluate : 2.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 457 LEU cc_start: 0.6203 (OUTLIER) cc_final: 0.5951 (mm) REVERT: E 602 TYR cc_start: 0.6102 (OUTLIER) cc_final: 0.5700 (p90) outliers start: 89 outliers final: 81 residues processed: 557 average time/residue: 0.7165 time to fit residues: 584.3802 Evaluate side-chains 577 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 494 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 521 THR Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 64 LEU Chi-restraints excluded: chain B residue 72 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 255 GLU Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 379 ASN Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 451 ILE Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 486 MET Chi-restraints excluded: chain B residue 504 ARG Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 112 LYS Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 313 GLU Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 379 ASN Chi-restraints excluded: chain C residue 386 VAL Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 400 ILE Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 313 GLU Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain D residue 510 ASP Chi-restraints excluded: chain D residue 521 THR Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain E residue 602 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 0.0870 chunk 139 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 moved from start: 0.8809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17176 Z= 0.179 Angle : 0.562 7.437 23268 Z= 0.303 Chirality : 0.042 0.387 2584 Planarity : 0.005 0.069 3088 Dihedral : 4.738 20.165 2316 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.10 % Allowed : 24.72 % Favored : 72.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.18), residues: 2124 helix: 0.50 (0.18), residues: 774 sheet: -0.78 (0.22), residues: 456 loop : -0.38 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 529 HIS 0.007 0.001 HIS C 498 PHE 0.037 0.002 PHE A 323 TYR 0.025 0.001 TYR D 455 ARG 0.010 0.001 ARG C 195 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 546 time to evaluate : 2.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 43 LEU cc_start: 0.7998 (tp) cc_final: 0.7655 (tt) REVERT: D 192 LEU cc_start: 0.6730 (mt) cc_final: 0.6042 (mt) REVERT: E 602 TYR cc_start: 0.5873 (OUTLIER) cc_final: 0.5500 (p90) outliers start: 56 outliers final: 49 residues processed: 565 average time/residue: 0.7355 time to fit residues: 603.3728 Evaluate side-chains 572 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 522 time to evaluate : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 451 ILE Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain E residue 602 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 0.7980 chunk 178 optimal weight: 5.9990 chunk 190 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 moved from start: 0.8948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17176 Z= 0.176 Angle : 0.556 6.528 23268 Z= 0.300 Chirality : 0.042 0.392 2584 Planarity : 0.005 0.104 3088 Dihedral : 4.539 19.888 2316 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.55 % Allowed : 26.05 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2124 helix: 0.80 (0.18), residues: 774 sheet: -0.76 (0.22), residues: 458 loop : -0.27 (0.21), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 529 HIS 0.008 0.001 HIS B 498 PHE 0.027 0.001 PHE D 323 TYR 0.034 0.001 TYR C 489 ARG 0.016 0.001 ARG C 195 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 528 time to evaluate : 2.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 452 GLN cc_start: 0.4905 (tp40) cc_final: 0.4681 (tp40) REVERT: D 43 LEU cc_start: 0.8007 (tp) cc_final: 0.7648 (tt) REVERT: D 268 ASN cc_start: 0.4938 (t0) cc_final: 0.4708 (t0) REVERT: D 313 GLU cc_start: 0.5911 (mp0) cc_final: 0.5702 (mp0) REVERT: E 602 TYR cc_start: 0.5873 (OUTLIER) cc_final: 0.5479 (p90) outliers start: 46 outliers final: 43 residues processed: 543 average time/residue: 0.7252 time to fit residues: 563.7431 Evaluate side-chains 568 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 524 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 72 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain E residue 602 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 139 optimal weight: 0.9990 chunk 211 optimal weight: 8.9990 chunk 194 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5430 moved from start: 0.9133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 17176 Z= 0.208 Angle : 0.568 7.009 23268 Z= 0.309 Chirality : 0.042 0.386 2584 Planarity : 0.005 0.095 3088 Dihedral : 4.537 19.887 2316 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.66 % Allowed : 26.00 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2124 helix: 0.70 (0.18), residues: 776 sheet: -0.76 (0.22), residues: 458 loop : -0.38 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 529 HIS 0.008 0.001 HIS B 498 PHE 0.024 0.002 PHE D 323 TYR 0.028 0.001 TYR C 489 ARG 0.015 0.001 ARG C 195 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4248 Ramachandran restraints generated. 2124 Oldfield, 0 Emsley, 2124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 520 time to evaluate : 2.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 192 LEU cc_start: 0.6556 (mt) cc_final: 0.6278 (mt) REVERT: D 313 GLU cc_start: 0.5989 (mp0) cc_final: 0.5787 (mp0) REVERT: E 602 TYR cc_start: 0.5885 (OUTLIER) cc_final: 0.5465 (p90) outliers start: 48 outliers final: 46 residues processed: 538 average time/residue: 0.7310 time to fit residues: 568.7958 Evaluate side-chains 557 residues out of total 1804 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 510 time to evaluate : 2.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 456 TYR Chi-restraints excluded: chain B residue 31 ARG Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 80 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 306 TRP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 468 ASP Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 31 ARG Chi-restraints excluded: chain C residue 56 GLN Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 142 ILE Chi-restraints excluded: chain C residue 154 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 306 TRP Chi-restraints excluded: chain C residue 345 MET Chi-restraints excluded: chain C residue 397 ASN Chi-restraints excluded: chain C residue 468 ASP Chi-restraints excluded: chain C residue 486 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 69 ASP Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 346 ARG Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 381 VAL Chi-restraints excluded: chain D residue 456 TYR Chi-restraints excluded: chain D residue 457 LEU Chi-restraints excluded: chain E residue 602 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN ** A 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 439 ASN ** B 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.148116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.126229 restraints weight = 138504.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130852 restraints weight = 66901.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.134041 restraints weight = 40220.585| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.9389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17176 Z= 0.215 Angle : 0.572 7.175 23268 Z= 0.312 Chirality : 0.042 0.383 2584 Planarity : 0.005 0.098 3088 Dihedral : 4.553 19.655 2316 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.88 % Allowed : 26.22 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.18), residues: 2124 helix: 0.59 (0.18), residues: 790 sheet: -0.79 (0.22), residues: 458 loop : -0.42 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP D 529 HIS 0.008 0.001 HIS B 498 PHE 0.024 0.002 PHE A 323 TYR 0.019 0.001 TYR C 489 ARG 0.014 0.001 ARG A 526 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10707.08 seconds wall clock time: 189 minutes 30.00 seconds (11370.00 seconds total)