Starting phenix.real_space_refine (version: dev) on Fri Dec 16 15:03:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/12_2022/7sn7_25213.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/12_2022/7sn7_25213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/12_2022/7sn7_25213.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/12_2022/7sn7_25213.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/12_2022/7sn7_25213.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sn7_25213/12_2022/7sn7_25213.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.070 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A GLU 84": "OE1" <-> "OE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A ASP 431": "OD1" <-> "OD2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 443": "OD1" <-> "OD2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "C ASP 141": "OD1" <-> "OD2" Residue "C ASP 370": "OD1" <-> "OD2" Residue "C PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 70": "OD1" <-> "OD2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D ASP 121": "OD1" <-> "OD2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 443": "OD1" <-> "OD2" Residue "E GLU 30": "OE1" <-> "OE2" Residue "E ASP 44": "OD1" <-> "OD2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 265": "OD1" <-> "OD2" Residue "E PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 431": "OD1" <-> "OD2" Residue "E TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 455": "OE1" <-> "OE2" Residue "E ASP 465": "OD1" <-> "OD2" Residue "F PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 381": "OD1" <-> "OD2" Residue "F TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 431": "OD1" <-> "OD2" Residue "F TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 514": "OE1" <-> "OE2" Residue "G GLU 30": "OE1" <-> "OE2" Residue "G TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 486": "OD1" <-> "OD2" Residue "H ASP 44": "OD1" <-> "OD2" Residue "H GLU 84": "OE1" <-> "OE2" Residue "H TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 30": "OE1" <-> "OE2" Residue "I ASP 164": "OD1" <-> "OD2" Residue "I ASP 166": "OD1" <-> "OD2" Residue "I ASP 220": "OD1" <-> "OD2" Residue "I TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 455": "OE1" <-> "OE2" Residue "I ASP 486": "OD1" <-> "OD2" Residue "I GLU 501": "OE1" <-> "OE2" Residue "J ASP 44": "OD1" <-> "OD2" Residue "J PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 166": "OD1" <-> "OD2" Residue "J GLU 180": "OE1" <-> "OE2" Residue "J TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 413": "OD1" <-> "OD2" Residue "J GLU 430": "OE1" <-> "OE2" Residue "J ASP 486": "OD1" <-> "OD2" Residue "J GLU 514": "OE1" <-> "OE2" Residue "K GLU 115": "OE1" <-> "OE2" Residue "K PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 94": "OE1" <-> "OE2" Residue "L ASP 108": "OD1" <-> "OD2" Residue "L ASP 124": "OD1" <-> "OD2" Residue "L TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 30": "OE1" <-> "OE2" Residue "M TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 501": "OE1" <-> "OE2" Residue "M TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 44": "OD1" <-> "OD2" Residue "N PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 79": "OE1" <-> "OE2" Residue "N ASP 264": "OD1" <-> "OD2" Residue "N PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 472": "OD1" <-> "OD2" Residue "O GLU 30": "OE1" <-> "OE2" Residue "O GLU 84": "OE1" <-> "OE2" Residue "O GLU 115": "OE1" <-> "OE2" Residue "O GLU 180": "OE1" <-> "OE2" Residue "O PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 455": "OE1" <-> "OE2" Residue "O GLU 514": "OE1" <-> "OE2" Residue "a ASP 44": "OD1" <-> "OD2" Residue "a GLU 79": "OE1" <-> "OE2" Residue "a ASP 110": "OD1" <-> "OD2" Residue "a PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 486": "OD1" <-> "OD2" Residue "b GLU 30": "OE1" <-> "OE2" Residue "b ASP 44": "OD1" <-> "OD2" Residue "b ASP 70": "OD1" <-> "OD2" Residue "b ASP 159": "OD1" <-> "OD2" Residue "b TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 455": "OE1" <-> "OE2" Residue "b TYR 511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 44": "OD1" <-> "OD2" Residue "d ASP 141": "OD1" <-> "OD2" Residue "d TYR 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 413": "OD1" <-> "OD2" Residue "d TYR 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 486": "OD1" <-> "OD2" Residue "d GLU 501": "OE1" <-> "OE2" Residue "e GLU 79": "OE1" <-> "OE2" Residue "e GLU 84": "OE1" <-> "OE2" Residue "e ASP 114": "OD1" <-> "OD2" Residue "e PHE 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 431": "OD1" <-> "OD2" Residue "f GLU 84": "OE1" <-> "OE2" Residue "f ASP 114": "OD1" <-> "OD2" Residue "f TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 293": "OD1" <-> "OD2" Residue "f ASP 381": "OD1" <-> "OD2" Residue "f TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 501": "OE1" <-> "OE2" Residue "g GLU 94": "OE1" <-> "OE2" Residue "g ASP 141": "OD1" <-> "OD2" Residue "g ASP 166": "OD1" <-> "OD2" Residue "g TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 486": "OD1" <-> "OD2" Residue "g GLU 514": "OE1" <-> "OE2" Residue "h GLU 84": "OE1" <-> "OE2" Residue "h ASP 141": "OD1" <-> "OD2" Residue "h GLU 455": "OE1" <-> "OE2" Residue "h PHE 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 90482 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "B" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "C" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "D" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "E" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "F" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "G" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "H" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "I" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "J" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "K" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "L" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "M" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "N" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "O" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "a" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "b" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "c" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "d" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "e" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "f" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "g" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Chain: "h" Number of atoms: 3934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 3934 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 538} Time building chain proxies: 37.19, per 1000 atoms: 0.41 Number of scatterers: 90482 At special positions: 0 Unit cell: (251.64, 231.12, 341.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 138 16.00 O 20010 8.00 N 15778 7.00 C 54556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 31.23 Conformation dependent library (CDL) restraints added in 10.9 seconds 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23092 Finding SS restraints... Secondary structure from input PDB file: 273 helices and 196 sheets defined 44.8% alpha, 7.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.60 Creating SS restraints... Processing helix chain 'A' and resid 10 through 35 removed outlier: 3.713A pdb=" N SER A 23 " --> pdb=" O ASN A 19 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 100 Processing helix chain 'A' and resid 105 through 130 removed outlier: 3.538A pdb=" N THR A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 Processing helix chain 'A' and resid 187 through 191 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.615A pdb=" N ALA A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 Processing helix chain 'A' and resid 333 through 345 removed outlier: 3.648A pdb=" N THR A 339 " --> pdb=" O ALA A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 459 through 507 removed outlier: 3.530A pdb=" N ILE A 506 " --> pdb=" O ALA A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 538 removed outlier: 3.657A pdb=" N SER A 516 " --> pdb=" O ALA A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.509A pdb=" N GLN A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 3.805A pdb=" N THR B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER B 23 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALA B 24 " --> pdb=" O LYS B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 100 Processing helix chain 'B' and resid 105 through 130 Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 217 through 228 removed outlier: 3.796A pdb=" N ALA B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 276 Processing helix chain 'B' and resid 333 through 345 removed outlier: 3.594A pdb=" N THR B 339 " --> pdb=" O ALA B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 459 through 507 removed outlier: 3.925A pdb=" N ILE B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 537 removed outlier: 3.889A pdb=" N SER B 516 " --> pdb=" O ALA B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'C' and resid 10 through 35 removed outlier: 4.001A pdb=" N THR C 14 " --> pdb=" O LEU C 10 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 23 " --> pdb=" O ASN C 19 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 100 Processing helix chain 'C' and resid 105 through 130 Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 187 through 191 Processing helix chain 'C' and resid 217 through 228 removed outlier: 3.696A pdb=" N ALA C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 275 Processing helix chain 'C' and resid 333 through 345 removed outlier: 4.113A pdb=" N THR C 339 " --> pdb=" O ALA C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 459 through 505 removed outlier: 3.749A pdb=" N ALA C 463 " --> pdb=" O ASP C 459 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 464 " --> pdb=" O PRO C 460 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 505 " --> pdb=" O GLU C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 510 through 537 removed outlier: 3.668A pdb=" N SER C 516 " --> pdb=" O ALA C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 547 removed outlier: 4.255A pdb=" N LEU C 543 " --> pdb=" O PRO C 539 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN C 547 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 35 removed outlier: 3.697A pdb=" N THR D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 23 " --> pdb=" O ASN D 19 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 100 Processing helix chain 'D' and resid 105 through 130 Processing helix chain 'D' and resid 164 through 169 Processing helix chain 'D' and resid 187 through 191 Processing helix chain 'D' and resid 217 through 228 removed outlier: 3.629A pdb=" N ALA D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 276 Processing helix chain 'D' and resid 333 through 345 removed outlier: 3.629A pdb=" N THR D 339 " --> pdb=" O ALA D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 459 through 507 removed outlier: 3.544A pdb=" N ARG D 505 " --> pdb=" O GLU D 501 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE D 506 " --> pdb=" O ALA D 502 " (cutoff:3.500A) Processing helix chain 'D' and resid 510 through 537 removed outlier: 3.747A pdb=" N SER D 516 " --> pdb=" O ALA D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 547 Processing helix chain 'E' and resid 10 through 35 removed outlier: 3.772A pdb=" N THR E 14 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER E 23 " --> pdb=" O ASN E 19 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA E 24 " --> pdb=" O LYS E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 100 Processing helix chain 'E' and resid 105 through 130 removed outlier: 3.570A pdb=" N THR E 130 " --> pdb=" O VAL E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'E' and resid 217 through 228 removed outlier: 3.769A pdb=" N ALA E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 276 Processing helix chain 'E' and resid 333 through 345 removed outlier: 3.935A pdb=" N THR E 339 " --> pdb=" O ALA E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 459 through 505 removed outlier: 4.121A pdb=" N ASP E 466 " --> pdb=" O ALA E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 537 removed outlier: 3.549A pdb=" N GLU E 514 " --> pdb=" O ASP E 510 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER E 516 " --> pdb=" O ALA E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 547 Processing helix chain 'F' and resid 10 through 35 removed outlier: 3.691A pdb=" N THR F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 23 " --> pdb=" O ASN F 19 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA F 24 " --> pdb=" O LYS F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 100 Processing helix chain 'F' and resid 105 through 130 Processing helix chain 'F' and resid 164 through 169 Processing helix chain 'F' and resid 187 through 191 Processing helix chain 'F' and resid 217 through 228 removed outlier: 3.780A pdb=" N ALA F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 333 through 345 removed outlier: 3.651A pdb=" N THR F 339 " --> pdb=" O ALA F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 459 through 507 removed outlier: 3.640A pdb=" N ILE F 506 " --> pdb=" O ALA F 502 " (cutoff:3.500A) Processing helix chain 'F' and resid 510 through 537 removed outlier: 3.840A pdb=" N SER F 516 " --> pdb=" O ALA F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 540 through 547 Processing helix chain 'G' and resid 10 through 35 removed outlier: 3.870A pdb=" N THR G 14 " --> pdb=" O LEU G 10 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER G 23 " --> pdb=" O ASN G 19 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ALA G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 100 Processing helix chain 'G' and resid 105 through 130 Processing helix chain 'G' and resid 164 through 169 Processing helix chain 'G' and resid 217 through 228 removed outlier: 3.571A pdb=" N ALA G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 276 Processing helix chain 'G' and resid 333 through 345 removed outlier: 4.172A pdb=" N THR G 339 " --> pdb=" O ALA G 335 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 379 through 381 No H-bonds generated for 'chain 'G' and resid 379 through 381' Processing helix chain 'G' and resid 459 through 505 removed outlier: 3.603A pdb=" N ALA G 463 " --> pdb=" O ASP G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 510 through 537 removed outlier: 3.602A pdb=" N GLU G 514 " --> pdb=" O ASP G 510 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER G 516 " --> pdb=" O ALA G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 547 Processing helix chain 'H' and resid 10 through 35 removed outlier: 3.595A pdb=" N SER H 23 " --> pdb=" O ASN H 19 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA H 24 " --> pdb=" O LYS H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 100 Processing helix chain 'H' and resid 105 through 130 removed outlier: 3.579A pdb=" N THR H 130 " --> pdb=" O VAL H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 169 Processing helix chain 'H' and resid 187 through 191 Processing helix chain 'H' and resid 217 through 228 removed outlier: 3.536A pdb=" N ALA H 228 " --> pdb=" O ALA H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 276 Processing helix chain 'H' and resid 333 through 345 removed outlier: 3.546A pdb=" N THR H 339 " --> pdb=" O ALA H 335 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 459 through 507 removed outlier: 3.691A pdb=" N ILE H 506 " --> pdb=" O ALA H 502 " (cutoff:3.500A) Processing helix chain 'H' and resid 510 through 537 removed outlier: 4.031A pdb=" N GLU H 514 " --> pdb=" O ASP H 510 " (cutoff:3.500A) Processing helix chain 'H' and resid 540 through 546 Processing helix chain 'I' and resid 10 through 35 removed outlier: 3.707A pdb=" N THR I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER I 23 " --> pdb=" O ASN I 19 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA I 24 " --> pdb=" O LYS I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 100 Processing helix chain 'I' and resid 105 through 130 Processing helix chain 'I' and resid 164 through 169 Processing helix chain 'I' and resid 187 through 191 Processing helix chain 'I' and resid 217 through 228 removed outlier: 3.743A pdb=" N ALA I 228 " --> pdb=" O ALA I 224 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 276 removed outlier: 3.563A pdb=" N ASN I 276 " --> pdb=" O ALA I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 333 through 345 removed outlier: 3.572A pdb=" N THR I 339 " --> pdb=" O ALA I 335 " (cutoff:3.500A) Processing helix chain 'I' and resid 370 through 378 Processing helix chain 'I' and resid 459 through 505 removed outlier: 3.776A pdb=" N ALA I 463 " --> pdb=" O ASP I 459 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU I 464 " --> pdb=" O PRO I 460 " (cutoff:3.500A) Processing helix chain 'I' and resid 510 through 537 removed outlier: 3.617A pdb=" N SER I 516 " --> pdb=" O ALA I 512 " (cutoff:3.500A) Processing helix chain 'I' and resid 540 through 547 Processing helix chain 'J' and resid 10 through 35 removed outlier: 3.915A pdb=" N THR J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER J 23 " --> pdb=" O ASN J 19 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA J 24 " --> pdb=" O LYS J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 100 Processing helix chain 'J' and resid 105 through 130 Processing helix chain 'J' and resid 164 through 169 Processing helix chain 'J' and resid 187 through 191 Processing helix chain 'J' and resid 217 through 228 removed outlier: 3.661A pdb=" N ALA J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 276 Processing helix chain 'J' and resid 333 through 345 removed outlier: 3.680A pdb=" N THR J 339 " --> pdb=" O ALA J 335 " (cutoff:3.500A) Processing helix chain 'J' and resid 370 through 378 Processing helix chain 'J' and resid 459 through 505 Processing helix chain 'J' and resid 510 through 537 removed outlier: 3.829A pdb=" N SER J 516 " --> pdb=" O ALA J 512 " (cutoff:3.500A) Processing helix chain 'J' and resid 540 through 547 Processing helix chain 'K' and resid 10 through 35 removed outlier: 3.762A pdb=" N THR K 14 " --> pdb=" O LEU K 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER K 23 " --> pdb=" O ASN K 19 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA K 24 " --> pdb=" O LYS K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 100 Processing helix chain 'K' and resid 105 through 130 removed outlier: 3.655A pdb=" N THR K 130 " --> pdb=" O VAL K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 169 Processing helix chain 'K' and resid 187 through 191 Processing helix chain 'K' and resid 217 through 228 removed outlier: 3.519A pdb=" N ALA K 228 " --> pdb=" O ALA K 224 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 276 Processing helix chain 'K' and resid 333 through 345 removed outlier: 3.617A pdb=" N THR K 339 " --> pdb=" O ALA K 335 " (cutoff:3.500A) Processing helix chain 'K' and resid 370 through 379 Processing helix chain 'K' and resid 459 through 507 Processing helix chain 'K' and resid 510 through 538 removed outlier: 3.541A pdb=" N GLU K 514 " --> pdb=" O ASP K 510 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER K 516 " --> pdb=" O ALA K 512 " (cutoff:3.500A) Processing helix chain 'K' and resid 540 through 547 removed outlier: 3.554A pdb=" N GLN K 547 " --> pdb=" O LEU K 543 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 35 removed outlier: 3.756A pdb=" N THR L 14 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER L 23 " --> pdb=" O ASN L 19 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA L 24 " --> pdb=" O LYS L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 100 Processing helix chain 'L' and resid 105 through 130 removed outlier: 3.525A pdb=" N THR L 130 " --> pdb=" O VAL L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 169 Processing helix chain 'L' and resid 187 through 191 Processing helix chain 'L' and resid 217 through 228 Processing helix chain 'L' and resid 270 through 276 Processing helix chain 'L' and resid 333 through 345 removed outlier: 3.546A pdb=" N THR L 339 " --> pdb=" O ALA L 335 " (cutoff:3.500A) Processing helix chain 'L' and resid 370 through 378 Processing helix chain 'L' and resid 459 through 505 removed outlier: 3.580A pdb=" N ALA L 463 " --> pdb=" O ASP L 459 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG L 505 " --> pdb=" O GLU L 501 " (cutoff:3.500A) Processing helix chain 'L' and resid 510 through 537 removed outlier: 3.727A pdb=" N SER L 516 " --> pdb=" O ALA L 512 " (cutoff:3.500A) Processing helix chain 'L' and resid 540 through 547 Processing helix chain 'M' and resid 10 through 35 removed outlier: 3.813A pdb=" N THR M 14 " --> pdb=" O LEU M 10 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER M 23 " --> pdb=" O ASN M 19 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA M 24 " --> pdb=" O LYS M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 100 Processing helix chain 'M' and resid 105 through 130 Processing helix chain 'M' and resid 136 through 140 removed outlier: 3.668A pdb=" N ALA M 139 " --> pdb=" O ASN M 136 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LYS M 140 " --> pdb=" O VAL M 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 136 through 140' Processing helix chain 'M' and resid 164 through 169 Processing helix chain 'M' and resid 217 through 228 removed outlier: 3.644A pdb=" N ALA M 228 " --> pdb=" O ALA M 224 " (cutoff:3.500A) Processing helix chain 'M' and resid 270 through 276 Processing helix chain 'M' and resid 333 through 345 removed outlier: 3.835A pdb=" N THR M 339 " --> pdb=" O ALA M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 370 through 379 Processing helix chain 'M' and resid 459 through 507 Processing helix chain 'M' and resid 510 through 537 removed outlier: 3.558A pdb=" N GLU M 514 " --> pdb=" O ASP M 510 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER M 516 " --> pdb=" O ALA M 512 " (cutoff:3.500A) Processing helix chain 'M' and resid 540 through 547 removed outlier: 3.728A pdb=" N GLN M 547 " --> pdb=" O LEU M 543 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 35 removed outlier: 3.661A pdb=" N SER N 23 " --> pdb=" O ASN N 19 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA N 24 " --> pdb=" O LYS N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 100 Processing helix chain 'N' and resid 105 through 130 removed outlier: 3.572A pdb=" N THR N 130 " --> pdb=" O VAL N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 169 Processing helix chain 'N' and resid 187 through 191 Processing helix chain 'N' and resid 217 through 228 removed outlier: 3.663A pdb=" N ALA N 228 " --> pdb=" O ALA N 224 " (cutoff:3.500A) Processing helix chain 'N' and resid 270 through 276 Processing helix chain 'N' and resid 333 through 345 Processing helix chain 'N' and resid 370 through 378 Processing helix chain 'N' and resid 459 through 507 removed outlier: 3.516A pdb=" N ALA N 463 " --> pdb=" O ASP N 459 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE N 506 " --> pdb=" O ALA N 502 " (cutoff:3.500A) Processing helix chain 'N' and resid 510 through 537 removed outlier: 3.769A pdb=" N SER N 516 " --> pdb=" O ALA N 512 " (cutoff:3.500A) Processing helix chain 'N' and resid 540 through 547 Processing helix chain 'O' and resid 10 through 35 removed outlier: 3.891A pdb=" N THR O 14 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER O 23 " --> pdb=" O ASN O 19 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ALA O 24 " --> pdb=" O LYS O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 100 Processing helix chain 'O' and resid 105 through 130 removed outlier: 3.552A pdb=" N THR O 130 " --> pdb=" O VAL O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 191 removed outlier: 3.823A pdb=" N MET O 191 " --> pdb=" O LEU O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 217 through 228 removed outlier: 3.781A pdb=" N ALA O 228 " --> pdb=" O ALA O 224 " (cutoff:3.500A) Processing helix chain 'O' and resid 270 through 276 Processing helix chain 'O' and resid 333 through 345 removed outlier: 3.549A pdb=" N THR O 339 " --> pdb=" O ALA O 335 " (cutoff:3.500A) Processing helix chain 'O' and resid 370 through 379 Processing helix chain 'O' and resid 459 through 507 removed outlier: 3.560A pdb=" N ILE O 506 " --> pdb=" O ALA O 502 " (cutoff:3.500A) Processing helix chain 'O' and resid 510 through 537 removed outlier: 3.558A pdb=" N GLU O 514 " --> pdb=" O ASP O 510 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER O 516 " --> pdb=" O ALA O 512 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 547 Processing helix chain 'a' and resid 10 through 35 removed outlier: 3.680A pdb=" N SER a 23 " --> pdb=" O ASN a 19 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA a 24 " --> pdb=" O LYS a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 100 Processing helix chain 'a' and resid 105 through 130 Processing helix chain 'a' and resid 164 through 169 Processing helix chain 'a' and resid 217 through 228 removed outlier: 3.845A pdb=" N ALA a 228 " --> pdb=" O ALA a 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 270 through 276 Processing helix chain 'a' and resid 333 through 345 removed outlier: 3.627A pdb=" N THR a 339 " --> pdb=" O ALA a 335 " (cutoff:3.500A) Processing helix chain 'a' and resid 370 through 378 Processing helix chain 'a' and resid 459 through 505 Processing helix chain 'a' and resid 510 through 537 removed outlier: 3.799A pdb=" N GLU a 514 " --> pdb=" O ASP a 510 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER a 516 " --> pdb=" O ALA a 512 " (cutoff:3.500A) Processing helix chain 'a' and resid 540 through 547 Processing helix chain 'b' and resid 10 through 35 removed outlier: 3.997A pdb=" N THR b 14 " --> pdb=" O LEU b 10 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER b 23 " --> pdb=" O ASN b 19 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA b 24 " --> pdb=" O LYS b 20 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 100 Processing helix chain 'b' and resid 105 through 129 Processing helix chain 'b' and resid 164 through 169 Processing helix chain 'b' and resid 187 through 191 Processing helix chain 'b' and resid 217 through 228 removed outlier: 3.719A pdb=" N ALA b 228 " --> pdb=" O ALA b 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 270 through 276 removed outlier: 3.573A pdb=" N ASN b 276 " --> pdb=" O ALA b 272 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 345 removed outlier: 3.738A pdb=" N THR b 339 " --> pdb=" O ALA b 335 " (cutoff:3.500A) Processing helix chain 'b' and resid 370 through 378 Processing helix chain 'b' and resid 459 through 505 removed outlier: 3.826A pdb=" N ALA b 463 " --> pdb=" O ASP b 459 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU b 464 " --> pdb=" O PRO b 460 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG b 505 " --> pdb=" O GLU b 501 " (cutoff:3.500A) Processing helix chain 'b' and resid 510 through 537 removed outlier: 3.635A pdb=" N SER b 516 " --> pdb=" O ALA b 512 " (cutoff:3.500A) Processing helix chain 'b' and resid 540 through 547 Processing helix chain 'c' and resid 10 through 35 removed outlier: 3.507A pdb=" N SER c 23 " --> pdb=" O ASN c 19 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA c 24 " --> pdb=" O LYS c 20 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 100 Processing helix chain 'c' and resid 105 through 130 Processing helix chain 'c' and resid 164 through 169 Processing helix chain 'c' and resid 217 through 228 removed outlier: 3.650A pdb=" N ALA c 228 " --> pdb=" O ALA c 224 " (cutoff:3.500A) Processing helix chain 'c' and resid 270 through 276 Processing helix chain 'c' and resid 333 through 345 removed outlier: 3.625A pdb=" N THR c 339 " --> pdb=" O ALA c 335 " (cutoff:3.500A) Processing helix chain 'c' and resid 370 through 378 Processing helix chain 'c' and resid 459 through 507 removed outlier: 3.622A pdb=" N ALA c 463 " --> pdb=" O ASP c 459 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE c 506 " --> pdb=" O ALA c 502 " (cutoff:3.500A) Processing helix chain 'c' and resid 510 through 537 removed outlier: 3.826A pdb=" N SER c 516 " --> pdb=" O ALA c 512 " (cutoff:3.500A) Processing helix chain 'c' and resid 540 through 547 Processing helix chain 'd' and resid 10 through 35 removed outlier: 3.582A pdb=" N THR d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER d 23 " --> pdb=" O ASN d 19 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA d 24 " --> pdb=" O LYS d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 44 through 100 Processing helix chain 'd' and resid 105 through 130 Processing helix chain 'd' and resid 164 through 169 Processing helix chain 'd' and resid 187 through 191 Processing helix chain 'd' and resid 217 through 228 removed outlier: 3.516A pdb=" N ALA d 228 " --> pdb=" O ALA d 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 270 through 276 Processing helix chain 'd' and resid 333 through 345 removed outlier: 3.529A pdb=" N THR d 339 " --> pdb=" O ALA d 335 " (cutoff:3.500A) Processing helix chain 'd' and resid 370 through 378 Processing helix chain 'd' and resid 459 through 507 removed outlier: 3.731A pdb=" N ILE d 506 " --> pdb=" O ALA d 502 " (cutoff:3.500A) Processing helix chain 'd' and resid 510 through 537 removed outlier: 3.649A pdb=" N SER d 516 " --> pdb=" O ALA d 512 " (cutoff:3.500A) Processing helix chain 'd' and resid 539 through 547 removed outlier: 4.321A pdb=" N LEU d 543 " --> pdb=" O PRO d 539 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 35 removed outlier: 3.513A pdb=" N THR e 14 " --> pdb=" O LEU e 10 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER e 23 " --> pdb=" O ASN e 19 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA e 24 " --> pdb=" O LYS e 20 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 100 Processing helix chain 'e' and resid 105 through 130 removed outlier: 3.612A pdb=" N THR e 130 " --> pdb=" O VAL e 126 " (cutoff:3.500A) Processing helix chain 'e' and resid 164 through 169 Processing helix chain 'e' and resid 187 through 191 removed outlier: 3.508A pdb=" N MET e 191 " --> pdb=" O LEU e 188 " (cutoff:3.500A) Processing helix chain 'e' and resid 217 through 228 removed outlier: 3.892A pdb=" N ALA e 228 " --> pdb=" O ALA e 224 " (cutoff:3.500A) Processing helix chain 'e' and resid 270 through 276 Processing helix chain 'e' and resid 333 through 345 removed outlier: 3.557A pdb=" N THR e 339 " --> pdb=" O ALA e 335 " (cutoff:3.500A) Processing helix chain 'e' and resid 370 through 378 Processing helix chain 'e' and resid 379 through 381 No H-bonds generated for 'chain 'e' and resid 379 through 381' Processing helix chain 'e' and resid 459 through 505 Processing helix chain 'e' and resid 510 through 538 removed outlier: 3.827A pdb=" N GLU e 514 " --> pdb=" O ASP e 510 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER e 516 " --> pdb=" O ALA e 512 " (cutoff:3.500A) Processing helix chain 'e' and resid 540 through 547 removed outlier: 3.709A pdb=" N GLN e 547 " --> pdb=" O LEU e 543 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 35 removed outlier: 3.891A pdb=" N THR f 14 " --> pdb=" O LEU f 10 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER f 23 " --> pdb=" O ASN f 19 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA f 24 " --> pdb=" O LYS f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 44 through 100 Processing helix chain 'f' and resid 105 through 130 Processing helix chain 'f' and resid 164 through 169 Processing helix chain 'f' and resid 187 through 191 Processing helix chain 'f' and resid 217 through 228 removed outlier: 3.761A pdb=" N ALA f 228 " --> pdb=" O ALA f 224 " (cutoff:3.500A) Processing helix chain 'f' and resid 270 through 276 Processing helix chain 'f' and resid 333 through 345 removed outlier: 3.708A pdb=" N THR f 339 " --> pdb=" O ALA f 335 " (cutoff:3.500A) Processing helix chain 'f' and resid 370 through 378 Processing helix chain 'f' and resid 459 through 507 removed outlier: 3.592A pdb=" N ALA f 463 " --> pdb=" O ASP f 459 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG f 505 " --> pdb=" O GLU f 501 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE f 506 " --> pdb=" O ALA f 502 " (cutoff:3.500A) Processing helix chain 'f' and resid 510 through 537 removed outlier: 3.616A pdb=" N GLU f 514 " --> pdb=" O ASP f 510 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER f 516 " --> pdb=" O ALA f 512 " (cutoff:3.500A) Processing helix chain 'f' and resid 540 through 547 removed outlier: 3.610A pdb=" N GLN f 547 " --> pdb=" O LEU f 543 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 35 removed outlier: 3.743A pdb=" N THR g 14 " --> pdb=" O LEU g 10 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER g 23 " --> pdb=" O ASN g 19 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA g 24 " --> pdb=" O LYS g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 100 Processing helix chain 'g' and resid 105 through 130 Processing helix chain 'g' and resid 164 through 169 Processing helix chain 'g' and resid 187 through 191 Processing helix chain 'g' and resid 217 through 228 removed outlier: 3.686A pdb=" N ALA g 228 " --> pdb=" O ALA g 224 " (cutoff:3.500A) Processing helix chain 'g' and resid 270 through 276 Processing helix chain 'g' and resid 333 through 345 removed outlier: 3.534A pdb=" N THR g 339 " --> pdb=" O ALA g 335 " (cutoff:3.500A) Processing helix chain 'g' and resid 370 through 378 Processing helix chain 'g' and resid 459 through 507 removed outlier: 3.507A pdb=" N LEU g 464 " --> pdb=" O PRO g 460 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE g 506 " --> pdb=" O ALA g 502 " (cutoff:3.500A) Processing helix chain 'g' and resid 510 through 537 removed outlier: 3.513A pdb=" N SER g 516 " --> pdb=" O ALA g 512 " (cutoff:3.500A) Processing helix chain 'g' and resid 539 through 547 removed outlier: 4.102A pdb=" N LEU g 543 " --> pdb=" O PRO g 539 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 35 removed outlier: 3.979A pdb=" N THR h 14 " --> pdb=" O LEU h 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER h 23 " --> pdb=" O ASN h 19 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA h 24 " --> pdb=" O LYS h 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 44 through 100 Processing helix chain 'h' and resid 105 through 130 Processing helix chain 'h' and resid 164 through 169 Processing helix chain 'h' and resid 217 through 228 Processing helix chain 'h' and resid 270 through 276 removed outlier: 3.617A pdb=" N PHE h 274 " --> pdb=" O ASN h 270 " (cutoff:3.500A) Processing helix chain 'h' and resid 333 through 345 removed outlier: 3.787A pdb=" N THR h 339 " --> pdb=" O ALA h 335 " (cutoff:3.500A) Processing helix chain 'h' and resid 370 through 378 Processing helix chain 'h' and resid 459 through 505 Processing helix chain 'h' and resid 510 through 537 removed outlier: 3.679A pdb=" N SER h 516 " --> pdb=" O ALA h 512 " (cutoff:3.500A) Processing helix chain 'h' and resid 539 through 547 removed outlier: 4.117A pdb=" N LEU h 543 " --> pdb=" O PRO h 539 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN h 547 " --> pdb=" O LEU h 543 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 143 through 147 Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 196 Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 288 Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 357 Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AA7, first strand: chain 'A' and resid 405 through 406 Processing sheet with id=AA8, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AA9, first strand: chain 'B' and resid 143 through 147 Processing sheet with id=AB1, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AB2, first strand: chain 'B' and resid 283 through 288 Processing sheet with id=AB3, first strand: chain 'B' and resid 314 through 315 removed outlier: 3.562A pdb=" N ASN B 324 " --> pdb=" O TYR B 314 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 355 through 357 Processing sheet with id=AB5, first strand: chain 'B' and resid 386 through 387 Processing sheet with id=AB6, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB7, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AB8, first strand: chain 'C' and resid 143 through 147 Processing sheet with id=AB9, first strand: chain 'C' and resid 179 through 182 removed outlier: 3.975A pdb=" N GLY C 179 " --> pdb=" O ALA C 454 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 194 through 196 Processing sheet with id=AC2, first strand: chain 'C' and resid 260 through 263 removed outlier: 5.765A pdb=" N ALA C 261 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N SER C 366 " --> pdb=" O ALA C 261 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 283 through 288 Processing sheet with id=AC4, first strand: chain 'C' and resid 314 through 315 removed outlier: 3.594A pdb=" N ASN C 324 " --> pdb=" O TYR C 314 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 386 through 387 Processing sheet with id=AC6, first strand: chain 'C' and resid 405 through 406 Processing sheet with id=AC7, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AC8, first strand: chain 'D' and resid 143 through 147 Processing sheet with id=AC9, first strand: chain 'D' and resid 181 through 182 removed outlier: 3.710A pdb=" N THR D 181 " --> pdb=" O SER D 452 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER D 452 " --> pdb=" O THR D 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 194 through 196 Processing sheet with id=AD2, first strand: chain 'D' and resid 283 through 288 Processing sheet with id=AD3, first strand: chain 'D' and resid 314 through 315 removed outlier: 3.706A pdb=" N ASN D 324 " --> pdb=" O TYR D 314 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 355 through 357 Processing sheet with id=AD5, first strand: chain 'D' and resid 386 through 387 Processing sheet with id=AD6, first strand: chain 'D' and resid 405 through 406 Processing sheet with id=AD7, first strand: chain 'E' and resid 143 through 147 Processing sheet with id=AD8, first strand: chain 'E' and resid 194 through 196 Processing sheet with id=AD9, first strand: chain 'E' and resid 260 through 261 Processing sheet with id=AE1, first strand: chain 'E' and resid 283 through 288 Processing sheet with id=AE2, first strand: chain 'E' and resid 314 through 315 Processing sheet with id=AE3, first strand: chain 'E' and resid 355 through 357 Processing sheet with id=AE4, first strand: chain 'E' and resid 386 through 387 Processing sheet with id=AE5, first strand: chain 'E' and resid 405 through 406 Processing sheet with id=AE6, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AE7, first strand: chain 'F' and resid 143 through 147 Processing sheet with id=AE8, first strand: chain 'F' and resid 194 through 196 Processing sheet with id=AE9, first strand: chain 'F' and resid 260 through 261 Processing sheet with id=AF1, first strand: chain 'F' and resid 283 through 288 Processing sheet with id=AF2, first strand: chain 'F' and resid 314 through 315 removed outlier: 3.606A pdb=" N ASN F 324 " --> pdb=" O TYR F 314 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 355 through 357 Processing sheet with id=AF4, first strand: chain 'F' and resid 386 through 387 Processing sheet with id=AF5, first strand: chain 'F' and resid 405 through 406 Processing sheet with id=AF6, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AF7, first strand: chain 'G' and resid 143 through 147 Processing sheet with id=AF8, first strand: chain 'G' and resid 179 through 182 removed outlier: 4.106A pdb=" N GLY G 179 " --> pdb=" O ALA G 454 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 194 through 196 Processing sheet with id=AG1, first strand: chain 'G' and resid 260 through 261 Processing sheet with id=AG2, first strand: chain 'G' and resid 283 through 288 Processing sheet with id=AG3, first strand: chain 'G' and resid 314 through 315 Processing sheet with id=AG4, first strand: chain 'G' and resid 355 through 357 Processing sheet with id=AG5, first strand: chain 'G' and resid 386 through 387 Processing sheet with id=AG6, first strand: chain 'G' and resid 405 through 406 Processing sheet with id=AG7, first strand: chain 'H' and resid 131 through 132 Processing sheet with id=AG8, first strand: chain 'H' and resid 143 through 147 Processing sheet with id=AG9, first strand: chain 'H' and resid 194 through 196 Processing sheet with id=AH1, first strand: chain 'H' and resid 260 through 261 Processing sheet with id=AH2, first strand: chain 'H' and resid 283 through 288 Processing sheet with id=AH3, first strand: chain 'H' and resid 314 through 315 removed outlier: 3.664A pdb=" N ASN H 324 " --> pdb=" O TYR H 314 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'H' and resid 355 through 357 Processing sheet with id=AH5, first strand: chain 'H' and resid 386 through 387 Processing sheet with id=AH6, first strand: chain 'H' and resid 405 through 406 Processing sheet with id=AH7, first strand: chain 'I' and resid 143 through 147 Processing sheet with id=AH8, first strand: chain 'I' and resid 179 through 182 removed outlier: 4.149A pdb=" N GLY I 179 " --> pdb=" O ALA I 454 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'I' and resid 194 through 196 Processing sheet with id=AI1, first strand: chain 'I' and resid 260 through 261 Processing sheet with id=AI2, first strand: chain 'I' and resid 283 through 288 Processing sheet with id=AI3, first strand: chain 'I' and resid 314 through 315 Processing sheet with id=AI4, first strand: chain 'I' and resid 355 through 357 Processing sheet with id=AI5, first strand: chain 'I' and resid 382 through 383 Processing sheet with id=AI6, first strand: chain 'I' and resid 386 through 387 Processing sheet with id=AI7, first strand: chain 'I' and resid 405 through 406 Processing sheet with id=AI8, first strand: chain 'J' and resid 143 through 147 Processing sheet with id=AI9, first strand: chain 'J' and resid 194 through 196 Processing sheet with id=AJ1, first strand: chain 'J' and resid 260 through 261 Processing sheet with id=AJ2, first strand: chain 'J' and resid 283 through 288 Processing sheet with id=AJ3, first strand: chain 'J' and resid 314 through 315 removed outlier: 3.732A pdb=" N ASN J 324 " --> pdb=" O TYR J 314 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'J' and resid 355 through 357 Processing sheet with id=AJ5, first strand: chain 'J' and resid 386 through 387 Processing sheet with id=AJ6, first strand: chain 'J' and resid 405 through 406 Processing sheet with id=AJ7, first strand: chain 'K' and resid 143 through 147 Processing sheet with id=AJ8, first strand: chain 'K' and resid 194 through 196 Processing sheet with id=AJ9, first strand: chain 'K' and resid 283 through 288 Processing sheet with id=AK1, first strand: chain 'K' and resid 314 through 315 removed outlier: 4.041A pdb=" N ASN K 324 " --> pdb=" O TYR K 314 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'K' and resid 355 through 357 Processing sheet with id=AK3, first strand: chain 'K' and resid 386 through 387 Processing sheet with id=AK4, first strand: chain 'K' and resid 405 through 406 Processing sheet with id=AK5, first strand: chain 'L' and resid 131 through 132 Processing sheet with id=AK6, first strand: chain 'L' and resid 143 through 147 Processing sheet with id=AK7, first strand: chain 'L' and resid 181 through 182 removed outlier: 3.874A pdb=" N THR L 181 " --> pdb=" O SER L 452 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'L' and resid 194 through 196 Processing sheet with id=AK9, first strand: chain 'L' and resid 260 through 265 removed outlier: 3.529A pdb=" N MET L 367 " --> pdb=" O ALA L 261 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N SER L 263 " --> pdb=" O ALA L 365 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ALA L 365 " --> pdb=" O SER L 263 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASP L 265 " --> pdb=" O ASP L 363 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N ASP L 363 " --> pdb=" O ASP L 265 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'L' and resid 283 through 288 Processing sheet with id=AL2, first strand: chain 'L' and resid 314 through 315 Processing sheet with id=AL3, first strand: chain 'L' and resid 386 through 387 Processing sheet with id=AL4, first strand: chain 'L' and resid 405 through 406 Processing sheet with id=AL5, first strand: chain 'M' and resid 143 through 147 Processing sheet with id=AL6, first strand: chain 'M' and resid 194 through 196 Processing sheet with id=AL7, first strand: chain 'M' and resid 263 through 265 removed outlier: 3.579A pdb=" N SER M 263 " --> pdb=" O GLY M 364 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP M 265 " --> pdb=" O PHE M 362 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE M 362 " --> pdb=" O ASP M 265 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA M 361 " --> pdb=" O ASP M 358 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP M 358 " --> pdb=" O ALA M 361 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'M' and resid 283 through 288 Processing sheet with id=AL9, first strand: chain 'M' and resid 314 through 315 removed outlier: 3.940A pdb=" N ASN M 324 " --> pdb=" O TYR M 314 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'M' and resid 386 through 387 Processing sheet with id=AM2, first strand: chain 'M' and resid 405 through 406 Processing sheet with id=AM3, first strand: chain 'N' and resid 143 through 147 Processing sheet with id=AM4, first strand: chain 'N' and resid 181 through 182 removed outlier: 3.580A pdb=" N THR N 181 " --> pdb=" O SER N 452 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'N' and resid 194 through 196 Processing sheet with id=AM6, first strand: chain 'N' and resid 283 through 288 Processing sheet with id=AM7, first strand: chain 'N' and resid 314 through 315 removed outlier: 4.035A pdb=" N TYR N 314 " --> pdb=" O ASN N 324 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN N 324 " --> pdb=" O TYR N 314 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM7 Processing sheet with id=AM8, first strand: chain 'N' and resid 355 through 357 Processing sheet with id=AM9, first strand: chain 'N' and resid 386 through 387 Processing sheet with id=AN1, first strand: chain 'N' and resid 405 through 406 removed outlier: 3.592A pdb=" N TYR N 405 " --> pdb=" O SER N 412 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER N 412 " --> pdb=" O TYR N 405 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN1 Processing sheet with id=AN2, first strand: chain 'O' and resid 143 through 147 Processing sheet with id=AN3, first strand: chain 'O' and resid 194 through 196 removed outlier: 3.512A pdb=" N THR O 207 " --> pdb=" O ALA O 420 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'O' and resid 260 through 261 removed outlier: 3.571A pdb=" N MET O 367 " --> pdb=" O ALA O 261 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'O' and resid 283 through 288 Processing sheet with id=AN6, first strand: chain 'O' and resid 314 through 315 Processing sheet with id=AN7, first strand: chain 'O' and resid 355 through 357 Processing sheet with id=AN8, first strand: chain 'O' and resid 386 through 387 Processing sheet with id=AN9, first strand: chain 'O' and resid 405 through 406 Processing sheet with id=AO1, first strand: chain 'a' and resid 143 through 147 Processing sheet with id=AO2, first strand: chain 'a' and resid 194 through 196 Processing sheet with id=AO3, first strand: chain 'a' and resid 260 through 261 removed outlier: 3.718A pdb=" N MET a 367 " --> pdb=" O ALA a 261 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'a' and resid 283 through 288 Processing sheet with id=AO5, first strand: chain 'a' and resid 314 through 315 Processing sheet with id=AO6, first strand: chain 'a' and resid 355 through 357 Processing sheet with id=AO7, first strand: chain 'a' and resid 386 through 387 Processing sheet with id=AO8, first strand: chain 'a' and resid 405 through 406 Processing sheet with id=AO9, first strand: chain 'b' and resid 131 through 132 Processing sheet with id=AP1, first strand: chain 'b' and resid 143 through 147 Processing sheet with id=AP2, first strand: chain 'b' and resid 179 through 182 removed outlier: 3.988A pdb=" N GLY b 179 " --> pdb=" O ALA b 454 " (cutoff:3.500A) Processing sheet with id=AP3, first strand: chain 'b' and resid 194 through 196 Processing sheet with id=AP4, first strand: chain 'b' and resid 260 through 261 Processing sheet with id=AP5, first strand: chain 'b' and resid 283 through 288 Processing sheet with id=AP6, first strand: chain 'b' and resid 314 through 316 Processing sheet with id=AP7, first strand: chain 'b' and resid 355 through 357 Processing sheet with id=AP8, first strand: chain 'b' and resid 386 through 387 Processing sheet with id=AP9, first strand: chain 'b' and resid 405 through 406 Processing sheet with id=AQ1, first strand: chain 'c' and resid 143 through 147 Processing sheet with id=AQ2, first strand: chain 'c' and resid 194 through 196 Processing sheet with id=AQ3, first strand: chain 'c' and resid 260 through 261 Processing sheet with id=AQ4, first strand: chain 'c' and resid 283 through 288 Processing sheet with id=AQ5, first strand: chain 'c' and resid 314 through 315 removed outlier: 3.584A pdb=" N ASN c 324 " --> pdb=" O TYR c 314 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'c' and resid 355 through 357 Processing sheet with id=AQ7, first strand: chain 'c' and resid 386 through 387 Processing sheet with id=AQ8, first strand: chain 'c' and resid 405 through 406 Processing sheet with id=AQ9, first strand: chain 'd' and resid 143 through 147 Processing sheet with id=AR1, first strand: chain 'd' and resid 181 through 182 removed outlier: 4.640A pdb=" N THR d 181 " --> pdb=" O SER d 452 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER d 452 " --> pdb=" O THR d 181 " (cutoff:3.500A) No H-bonds generated for sheet with id=AR1 Processing sheet with id=AR2, first strand: chain 'd' and resid 194 through 196 Processing sheet with id=AR3, first strand: chain 'd' and resid 260 through 261 removed outlier: 3.542A pdb=" N ALA d 261 " --> pdb=" O MET d 367 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'd' and resid 283 through 288 Processing sheet with id=AR5, first strand: chain 'd' and resid 314 through 315 removed outlier: 3.508A pdb=" N ASN d 324 " --> pdb=" O TYR d 314 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'd' and resid 355 through 357 Processing sheet with id=AR7, first strand: chain 'd' and resid 382 through 383 Processing sheet with id=AR8, first strand: chain 'd' and resid 386 through 387 Processing sheet with id=AR9, first strand: chain 'd' and resid 405 through 406 Processing sheet with id=AS1, first strand: chain 'e' and resid 143 through 147 Processing sheet with id=AS2, first strand: chain 'e' and resid 194 through 196 Processing sheet with id=AS3, first strand: chain 'e' and resid 260 through 263 removed outlier: 5.542A pdb=" N SER e 263 " --> pdb=" O ALA e 365 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ALA e 365 " --> pdb=" O SER e 263 " (cutoff:3.500A) Processing sheet with id=AS4, first strand: chain 'e' and resid 283 through 288 Processing sheet with id=AS5, first strand: chain 'e' and resid 314 through 315 Processing sheet with id=AS6, first strand: chain 'e' and resid 386 through 387 Processing sheet with id=AS7, first strand: chain 'e' and resid 405 through 406 Processing sheet with id=AS8, first strand: chain 'f' and resid 143 through 147 Processing sheet with id=AS9, first strand: chain 'f' and resid 181 through 182 removed outlier: 3.521A pdb=" N SER f 452 " --> pdb=" O THR f 181 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'f' and resid 194 through 196 Processing sheet with id=AT2, first strand: chain 'f' and resid 260 through 261 Processing sheet with id=AT3, first strand: chain 'f' and resid 283 through 288 Processing sheet with id=AT4, first strand: chain 'f' and resid 314 through 316 Processing sheet with id=AT5, first strand: chain 'f' and resid 355 through 357 Processing sheet with id=AT6, first strand: chain 'f' and resid 386 through 387 Processing sheet with id=AT7, first strand: chain 'f' and resid 405 through 406 Processing sheet with id=AT8, first strand: chain 'g' and resid 131 through 132 Processing sheet with id=AT9, first strand: chain 'g' and resid 143 through 147 Processing sheet with id=AU1, first strand: chain 'g' and resid 179 through 182 removed outlier: 3.878A pdb=" N GLY g 179 " --> pdb=" O ALA g 454 " (cutoff:3.500A) Processing sheet with id=AU2, first strand: chain 'g' and resid 194 through 196 Processing sheet with id=AU3, first strand: chain 'g' and resid 283 through 288 Processing sheet with id=AU4, first strand: chain 'g' and resid 314 through 315 removed outlier: 3.604A pdb=" N ASN g 324 " --> pdb=" O TYR g 314 " (cutoff:3.500A) Processing sheet with id=AU5, first strand: chain 'g' and resid 355 through 357 Processing sheet with id=AU6, first strand: chain 'g' and resid 386 through 387 Processing sheet with id=AU7, first strand: chain 'g' and resid 405 through 406 Processing sheet with id=AU8, first strand: chain 'h' and resid 131 through 132 Processing sheet with id=AU9, first strand: chain 'h' and resid 143 through 147 Processing sheet with id=AV1, first strand: chain 'h' and resid 194 through 196 Processing sheet with id=AV2, first strand: chain 'h' and resid 260 through 261 Processing sheet with id=AV3, first strand: chain 'h' and resid 283 through 288 Processing sheet with id=AV4, first strand: chain 'h' and resid 314 through 315 removed outlier: 3.713A pdb=" N ASN h 324 " --> pdb=" O TYR h 314 " (cutoff:3.500A) Processing sheet with id=AV5, first strand: chain 'h' and resid 355 through 357 Processing sheet with id=AV6, first strand: chain 'h' and resid 386 through 387 Processing sheet with id=AV7, first strand: chain 'h' and resid 405 through 406 5083 hydrogen bonds defined for protein. 14637 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: 37.40 Time building geometry restraints manager: 33.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 29366 1.33 - 1.46: 11613 1.46 - 1.58: 49868 1.58 - 1.70: 3 1.70 - 1.82: 276 Bond restraints: 91126 Sorted by residual: bond pdb=" C ASP E 316 " pdb=" O ASP E 316 " ideal model delta sigma weight residual 1.236 1.267 -0.031 7.30e-03 1.88e+04 1.75e+01 bond pdb=" CA GLY C 179 " pdb=" C GLY C 179 " ideal model delta sigma weight residual 1.520 1.550 -0.030 7.30e-03 1.88e+04 1.67e+01 bond pdb=" CB PRO O 416 " pdb=" CG PRO O 416 " ideal model delta sigma weight residual 1.492 1.633 -0.141 5.00e-02 4.00e+02 7.97e+00 bond pdb=" CG LEU D 492 " pdb=" CD1 LEU D 492 " ideal model delta sigma weight residual 1.521 1.453 0.068 3.30e-02 9.18e+02 4.22e+00 bond pdb=" CB PRO c 416 " pdb=" CG PRO c 416 " ideal model delta sigma weight residual 1.492 1.592 -0.100 5.00e-02 4.00e+02 3.99e+00 ... (remaining 91121 not shown) Histogram of bond angle deviations from ideal: 98.97 - 105.30: 629 105.30 - 111.63: 43694 111.63 - 117.97: 26797 117.97 - 124.30: 52157 124.30 - 130.63: 601 Bond angle restraints: 123878 Sorted by residual: angle pdb=" CA PRO O 416 " pdb=" N PRO O 416 " pdb=" CD PRO O 416 " ideal model delta sigma weight residual 112.00 101.92 10.08 1.40e+00 5.10e-01 5.19e+01 angle pdb=" N ILE b 289 " pdb=" CA ILE b 289 " pdb=" C ILE b 289 " ideal model delta sigma weight residual 112.29 106.93 5.36 9.40e-01 1.13e+00 3.25e+01 angle pdb=" CA PRO c 416 " pdb=" N PRO c 416 " pdb=" CD PRO c 416 " ideal model delta sigma weight residual 112.00 105.45 6.55 1.40e+00 5.10e-01 2.19e+01 angle pdb=" N ILE B 5 " pdb=" CA ILE B 5 " pdb=" C ILE B 5 " ideal model delta sigma weight residual 106.21 110.86 -4.65 1.07e+00 8.73e-01 1.89e+01 angle pdb=" C GLY E 169 " pdb=" N LEU E 170 " pdb=" CA LEU E 170 " ideal model delta sigma weight residual 121.54 129.68 -8.14 1.91e+00 2.74e-01 1.82e+01 ... (remaining 123873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 50922 17.98 - 35.96: 3707 35.96 - 53.94: 536 53.94 - 71.92: 191 71.92 - 89.90: 51 Dihedral angle restraints: 55407 sinusoidal: 19504 harmonic: 35903 Sorted by residual: dihedral pdb=" CA VAL d 538 " pdb=" C VAL d 538 " pdb=" N PRO d 539 " pdb=" CA PRO d 539 " ideal model delta harmonic sigma weight residual -180.00 -147.35 -32.65 0 5.00e+00 4.00e-02 4.26e+01 dihedral pdb=" CA ASN D 176 " pdb=" C ASN D 176 " pdb=" N GLY D 177 " pdb=" CA GLY D 177 " ideal model delta harmonic sigma weight residual 180.00 -152.88 -27.12 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ILE K 5 " pdb=" C ILE K 5 " pdb=" N ASN K 6 " pdb=" CA ASN K 6 " ideal model delta harmonic sigma weight residual 180.00 153.26 26.74 0 5.00e+00 4.00e-02 2.86e+01 ... (remaining 55404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 13824 0.068 - 0.136: 1354 0.136 - 0.204: 64 0.204 - 0.272: 4 0.272 - 0.340: 3 Chirality restraints: 15249 Sorted by residual: chirality pdb=" CB THR L 457 " pdb=" CA THR L 457 " pdb=" OG1 THR L 457 " pdb=" CG2 THR L 457 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB THR D 457 " pdb=" CA THR D 457 " pdb=" OG1 THR D 457 " pdb=" CG2 THR D 457 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB THR N 457 " pdb=" CA THR N 457 " pdb=" OG1 THR N 457 " pdb=" CG2 THR N 457 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 15246 not shown) Planarity restraints: 16583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO c 415 " -0.085 5.00e-02 4.00e+02 1.24e-01 2.48e+01 pdb=" N PRO c 416 " 0.215 5.00e-02 4.00e+02 pdb=" CA PRO c 416 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO c 416 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO O 415 " 0.078 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO O 416 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO O 416 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO O 416 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO a 415 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO a 416 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO a 416 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO a 416 " -0.059 5.00e-02 4.00e+02 ... (remaining 16580 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1957 2.66 - 3.22: 95943 3.22 - 3.78: 141674 3.78 - 4.34: 176508 4.34 - 4.90: 291252 Nonbonded interactions: 707334 Sorted by model distance: nonbonded pdb=" OG SER h 258 " pdb=" O ILE h 369 " model vdw 2.099 2.440 nonbonded pdb=" OG1 THR I 234 " pdb=" OG1 THR I 384 " model vdw 2.107 2.440 nonbonded pdb=" OG1 THR F 234 " pdb=" OG1 THR F 384 " model vdw 2.107 2.440 nonbonded pdb=" OG SER C 258 " pdb=" O ILE C 369 " model vdw 2.112 2.440 nonbonded pdb=" OG SER B 258 " pdb=" O ILE B 369 " model vdw 2.122 2.440 ... (remaining 707329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = 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 Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 138 5.16 5 C 54556 2.51 5 N 15778 2.21 5 O 20010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.720 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: 0.070 Extract box with map and model: 18.220 Check model and map are aligned: 1.020 Convert atoms to be neutral: 0.610 Process input model: 185.820 Find NCS groups from input model: 5.060 Set up NCS constraints: 0.630 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 218.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 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 : 0.003 0.141 91126 Z= 0.190 Angle : 0.631 11.867 123878 Z= 0.346 Chirality : 0.040 0.340 15249 Planarity : 0.004 0.124 16583 Dihedral : 13.406 89.897 32315 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.08), residues: 12512 helix: 3.16 (0.07), residues: 5181 sheet: 0.55 (0.14), residues: 1357 loop : -2.30 (0.07), residues: 5974 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2316 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 2309 time to evaluate : 8.636 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 outliers start: 7 outliers final: 0 residues processed: 2316 average time/residue: 0.7665 time to fit residues: 3148.1631 Evaluate side-chains 1532 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1532 time to evaluate : 8.030 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.5560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1048 optimal weight: 20.0000 chunk 941 optimal weight: 20.0000 chunk 522 optimal weight: 9.9990 chunk 321 optimal weight: 6.9990 chunk 635 optimal weight: 0.0870 chunk 502 optimal weight: 0.9990 chunk 973 optimal weight: 7.9990 chunk 376 optimal weight: 4.9990 chunk 591 optimal weight: 7.9990 chunk 724 optimal weight: 8.9990 chunk 1127 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 39 ASN A 63 GLN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 ASN ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN B 498 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 GLN D 16 ASN D 52 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 57 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN ** F 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN ** G 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN ** G 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 376 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 ASN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 208 GLN ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN K 154 GLN K 331 GLN L 63 GLN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 ASN ** L 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 GLN N 376 ASN N 482 GLN ** O 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 ASN ** O 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 8 ASN ** a 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 223 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 507 GLN b 76 GLN ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 231 ASN b 294 GLN b 331 GLN ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN d 349 GLN ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 331 GLN e 529 ASN f 90 GLN f 113 GLN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 223 ASN ** f 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 ASN g 76 GLN g 278 GLN ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 6 ASN ** h 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 113 GLN ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 498 ASN h 541 GLN Total number of N/Q/H flips: 54 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 91126 Z= 0.265 Angle : 0.618 10.159 123878 Z= 0.337 Chirality : 0.040 0.256 15249 Planarity : 0.003 0.076 16583 Dihedral : 4.779 32.393 13110 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.50 (0.08), residues: 12512 helix: 2.93 (0.07), residues: 5343 sheet: 0.37 (0.13), residues: 1357 loop : -2.39 (0.07), residues: 5812 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1937 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1914 time to evaluate : 8.191 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 outliers start: 23 outliers final: 6 residues processed: 1933 average time/residue: 0.7650 time to fit residues: 2664.2003 Evaluate side-chains 1397 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1391 time to evaluate : 7.968 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.6230 time to fit residues: 17.7680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 626 optimal weight: 0.8980 chunk 350 optimal weight: 0.2980 chunk 938 optimal weight: 9.9990 chunk 768 optimal weight: 4.9990 chunk 311 optimal weight: 7.9990 chunk 1129 optimal weight: 4.9990 chunk 1220 optimal weight: 10.0000 chunk 1006 optimal weight: 5.9990 chunk 1120 optimal weight: 10.0000 chunk 385 optimal weight: 2.9990 chunk 906 optimal weight: 30.0000 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 17 ASN A 39 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN B 529 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 ASN ** D 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 52 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN G 525 GLN G 529 ASN H 3 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 GLN K 86 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 ASN ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 136 ASN ** M 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 529 ASN ** N 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 GLN ** N 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 48 GLN O 88 ASN ** O 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 491 ASN ** O 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 22 GLN ** a 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 GLN a 86 ASN ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 525 GLN ** b 537 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 GLN ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 276 ASN ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 ASN d 76 GLN ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN d 349 GLN ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 541 GLN f 19 ASN f 76 GLN f 98 GLN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 63 GLN ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 GLN ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 541 GLN ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 98 GLN ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 91126 Z= 0.219 Angle : 0.582 10.981 123878 Z= 0.317 Chirality : 0.039 0.258 15249 Planarity : 0.003 0.061 16583 Dihedral : 4.729 30.744 13110 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer Outliers : 0.14 % 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: 0.45 (0.08), residues: 12512 helix: 2.92 (0.07), residues: 5400 sheet: 0.14 (0.13), residues: 1381 loop : -2.47 (0.07), residues: 5731 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1906 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1892 time to evaluate : 8.752 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 outliers start: 14 outliers final: 6 residues processed: 1902 average time/residue: 0.7276 time to fit residues: 2475.2832 Evaluate side-chains 1385 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1379 time to evaluate : 7.945 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.6314 time to fit residues: 18.6790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1116 optimal weight: 10.0000 chunk 849 optimal weight: 30.0000 chunk 586 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 539 optimal weight: 3.9990 chunk 758 optimal weight: 10.0000 chunk 1133 optimal weight: 3.9990 chunk 1200 optimal weight: 2.9990 chunk 592 optimal weight: 1.9990 chunk 1074 optimal weight: 0.9990 chunk 323 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 331 GLN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN E 16 ASN ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN F 15 GLN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN ** F 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 15 GLN G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN H 3 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 491 ASN H 498 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 98 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN K 88 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 ASN N 278 GLN N 331 GLN ** O 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 526 GLN d 48 GLN ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN d 349 GLN d 537 GLN e 3 GLN ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 208 GLN e 276 ASN ** f 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 17 ASN ** g 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 91126 Z= 0.162 Angle : 0.553 11.226 123878 Z= 0.300 Chirality : 0.039 0.392 15249 Planarity : 0.003 0.051 16583 Dihedral : 4.527 31.539 13110 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.62 % 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: 0.56 (0.08), residues: 12512 helix: 3.03 (0.07), residues: 5442 sheet: 0.21 (0.14), residues: 1321 loop : -2.45 (0.07), residues: 5749 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1918 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1912 time to evaluate : 7.968 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 outliers start: 6 outliers final: 1 residues processed: 1917 average time/residue: 0.7264 time to fit residues: 2495.9751 Evaluate side-chains 1419 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1418 time to evaluate : 7.955 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7236 time to fit residues: 11.9770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 999 optimal weight: 5.9990 chunk 681 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 893 optimal weight: 6.9990 chunk 495 optimal weight: 10.0000 chunk 1024 optimal weight: 1.9990 chunk 829 optimal weight: 0.0980 chunk 1 optimal weight: 4.9990 chunk 613 optimal weight: 2.9990 chunk 1077 optimal weight: 5.9990 chunk 302 optimal weight: 20.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 39 ASN A 86 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN A 536 ASN B 39 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 ASN D 52 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN E 536 ASN F 6 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN ** F 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN a 113 GLN ** a 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 171 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 529 ASN ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 76 GLN ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 297 ASN ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 76 GLN ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 131 GLN ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 526 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 91126 Z= 0.237 Angle : 0.589 11.182 123878 Z= 0.319 Chirality : 0.040 0.380 15249 Planarity : 0.003 0.051 16583 Dihedral : 4.668 32.752 13110 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer Outliers : 0.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.45 (0.08), residues: 12512 helix: 2.97 (0.07), residues: 5394 sheet: 0.06 (0.13), residues: 1381 loop : -2.50 (0.07), residues: 5737 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1833 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1826 time to evaluate : 8.209 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 outliers start: 7 outliers final: 2 residues processed: 1829 average time/residue: 0.7210 time to fit residues: 2364.3836 Evaluate side-chains 1353 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1351 time to evaluate : 7.889 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6114 time to fit residues: 12.8523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 403 optimal weight: 5.9990 chunk 1081 optimal weight: 0.9980 chunk 237 optimal weight: 6.9990 chunk 704 optimal weight: 5.9990 chunk 296 optimal weight: 30.0000 chunk 1201 optimal weight: 5.9990 chunk 997 optimal weight: 0.2980 chunk 556 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 397 optimal weight: 10.0000 chunk 630 optimal weight: 5.9990 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN A 536 ASN B 39 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN C 86 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN C 349 GLN ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN ** F 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 297 ASN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN ** G 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 529 ASN ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 GLN ** O 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN a 171 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 331 GLN ** b 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 63 GLN ** c 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN ** e 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 208 GLN ** e 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 3 GLN ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 76 GLN ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 270 ASN f 331 GLN g 21 ASN ** g 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.3003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 91126 Z= 0.215 Angle : 0.583 11.165 123878 Z= 0.314 Chirality : 0.040 0.305 15249 Planarity : 0.003 0.048 16583 Dihedral : 4.655 31.751 13110 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer Outliers : 0.07 % 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: 0.42 (0.08), residues: 12512 helix: 2.98 (0.07), residues: 5385 sheet: -0.09 (0.14), residues: 1327 loop : -2.48 (0.07), residues: 5800 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1799 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1792 time to evaluate : 8.207 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 outliers start: 7 outliers final: 0 residues processed: 1796 average time/residue: 0.7382 time to fit residues: 2378.8679 Evaluate side-chains 1349 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1349 time to evaluate : 7.908 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.6188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1158 optimal weight: 40.0000 chunk 135 optimal weight: 0.0870 chunk 684 optimal weight: 20.0000 chunk 877 optimal weight: 9.9990 chunk 679 optimal weight: 8.9990 chunk 1011 optimal weight: 9.9990 chunk 671 optimal weight: 8.9990 chunk 1197 optimal weight: 0.9990 chunk 749 optimal weight: 10.0000 chunk 729 optimal weight: 7.9990 chunk 552 optimal weight: 9.9990 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 39 ASN A 63 GLN A 67 ASN A 86 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN B 39 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN C 86 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN ** C 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 16 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN G 15 GLN G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 3 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN H 498 ASN ** H 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 39 ASN ** I 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 522 GLN J 39 ASN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN M 136 ASN M 297 ASN ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 171 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 67 ASN c 98 GLN ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 297 ASN d 331 GLN ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 3 GLN e 15 GLN ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 76 GLN f 133 ASN ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 270 ASN ** f 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 22 GLN ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.079 91126 Z= 0.344 Angle : 0.692 11.334 123878 Z= 0.375 Chirality : 0.043 0.454 15249 Planarity : 0.004 0.060 16583 Dihedral : 5.239 37.512 13110 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.93 % Favored : 90.01 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.08), residues: 12512 helix: 2.59 (0.07), residues: 5325 sheet: -0.30 (0.14), residues: 1327 loop : -2.63 (0.07), residues: 5860 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1726 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1717 time to evaluate : 8.043 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 outliers start: 9 outliers final: 1 residues processed: 1722 average time/residue: 0.7320 time to fit residues: 2264.4560 Evaluate side-chains 1260 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1259 time to evaluate : 7.982 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7023 time to fit residues: 11.7313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 740 optimal weight: 3.9990 chunk 478 optimal weight: 0.8980 chunk 714 optimal weight: 1.9990 chunk 360 optimal weight: 30.0000 chunk 235 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 761 optimal weight: 4.9990 chunk 815 optimal weight: 0.8980 chunk 591 optimal weight: 4.9990 chunk 111 optimal weight: 20.0000 chunk 940 optimal weight: 20.0000 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** A 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 ASN B 39 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 491 ASN ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN D 52 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 16 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN G 15 GLN G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 529 ASN ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 183 ASN ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 483 ASN N 22 GLN N 331 GLN ** O 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 21 ASN ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 421 GLN ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 223 ASN f 270 ASN f 331 GLN ** g 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 57 ASN ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 498 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 91126 Z= 0.220 Angle : 0.615 10.692 123878 Z= 0.330 Chirality : 0.041 0.408 15249 Planarity : 0.003 0.049 16583 Dihedral : 4.965 33.349 13110 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.16 (0.08), residues: 12512 helix: 2.76 (0.07), residues: 5397 sheet: -0.29 (0.14), residues: 1327 loop : -2.61 (0.07), residues: 5788 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1760 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1752 time to evaluate : 8.147 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 outliers start: 8 outliers final: 2 residues processed: 1754 average time/residue: 0.7339 time to fit residues: 2300.8828 Evaluate side-chains 1287 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1285 time to evaluate : 8.379 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.6709 time to fit residues: 14.4187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 1088 optimal weight: 0.8980 chunk 1146 optimal weight: 5.9990 chunk 1046 optimal weight: 20.0000 chunk 1115 optimal weight: 3.9990 chunk 671 optimal weight: 7.9990 chunk 485 optimal weight: 5.9990 chunk 875 optimal weight: 4.9990 chunk 342 optimal weight: 0.0370 chunk 1008 optimal weight: 6.9990 chunk 1055 optimal weight: 8.9990 chunk 1111 optimal weight: 6.9990 overall best weight: 3.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 86 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN A 536 ASN B 39 ASN B 63 GLN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 525 GLN B 529 ASN ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN C 541 GLN D 52 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 491 ASN ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN F 16 ASN F 17 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 ASN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 ASN ** H 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 491 ASN I 522 GLN ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN ** M 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 15 GLN O 98 GLN O 278 GLN ** O 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 63 GLN a 86 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 GLN ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 526 GLN d 39 ASN ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN ** e 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 223 ASN f 270 ASN ** f 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 ASN ** g 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 253 ASN ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 91126 Z= 0.241 Angle : 0.627 12.053 123878 Z= 0.336 Chirality : 0.041 0.397 15249 Planarity : 0.003 0.049 16583 Dihedral : 4.945 32.037 13110 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 9.88 % Favored : 90.11 % Rotamer Outliers : 0.06 % 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: 0.14 (0.08), residues: 12512 helix: 2.79 (0.07), residues: 5355 sheet: -0.34 (0.14), residues: 1327 loop : -2.62 (0.07), residues: 5830 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1685 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1679 time to evaluate : 8.889 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 outliers start: 6 outliers final: 0 residues processed: 1681 average time/residue: 0.7415 time to fit residues: 2247.5036 Evaluate side-chains 1270 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1270 time to evaluate : 7.920 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 10.4457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 732 optimal weight: 30.0000 chunk 1179 optimal weight: 6.9990 chunk 719 optimal weight: 1.9990 chunk 559 optimal weight: 7.9990 chunk 820 optimal weight: 1.9990 chunk 1237 optimal weight: 0.7980 chunk 1138 optimal weight: 5.9990 chunk 985 optimal weight: 0.2980 chunk 102 optimal weight: 2.9990 chunk 761 optimal weight: 6.9990 chunk 604 optimal weight: 6.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN A 536 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN D 52 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 491 ASN G 52 ASN ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN H 3 GLN H 21 ASN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 529 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 529 ASN ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** K 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN M 48 GLN M 297 ASN ** N 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 331 GLN ** O 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 ASN ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN ** e 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 ASN ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 376 ASN ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 297 ASN ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 498 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 91126 Z= 0.186 Angle : 0.601 11.351 123878 Z= 0.321 Chirality : 0.040 0.359 15249 Planarity : 0.003 0.048 16583 Dihedral : 4.718 30.385 13110 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 0.28 (0.08), residues: 12512 helix: 2.91 (0.07), residues: 5388 sheet: -0.27 (0.14), residues: 1277 loop : -2.58 (0.07), residues: 5847 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25024 Ramachandran restraints generated. 12512 Oldfield, 0 Emsley, 12512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1722 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1716 time to evaluate : 8.028 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 outliers start: 6 outliers final: 1 residues processed: 1718 average time/residue: 0.7221 time to fit residues: 2236.7094 Evaluate side-chains 1298 residues out of total 9752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1297 time to evaluate : 8.139 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.6103 time to fit residues: 12.0549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1242 random chunks: chunk 782 optimal weight: 7.9990 chunk 1049 optimal weight: 7.9990 chunk 301 optimal weight: 10.0000 chunk 908 optimal weight: 0.3980 chunk 145 optimal weight: 8.9990 chunk 273 optimal weight: 20.0000 chunk 986 optimal weight: 9.9990 chunk 413 optimal weight: 2.9990 chunk 1013 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 overall best weight: 4.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 67 ASN A 86 ASN ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 470 GLN A 491 ASN A 536 ASN ** B 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 529 ASN ** B 541 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 21 ASN ** C 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN D 52 ASN ** D 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 ASN ** D 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 ASN F 17 ASN ** F 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 GLN F 491 ASN ** G 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 67 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 491 ASN H 3 GLN ** H 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 ASN ** H 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 278 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 86 ASN ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 547 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 ASN ** L 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 491 ASN M 136 ASN N 278 GLN ** N 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 208 GLN ** O 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 320 ASN a 86 ASN ** a 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 526 GLN d 39 ASN ** d 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 331 GLN ** d 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 48 GLN ** e 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 223 ASN f 270 ASN f 526 GLN g 21 ASN ** g 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN ** h 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 297 ASN ** h 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 526 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.151721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.118775 restraints weight = 190091.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.118008 restraints weight = 134129.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118782 restraints weight = 114317.417| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 91126 Z= 0.312 Angle : 0.680 11.298 123878 Z= 0.366 Chirality : 0.043 0.396 15249 Planarity : 0.003 0.050 16583 Dihedral : 5.150 37.745 13110 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.31 % Favored : 89.66 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.08), residues: 12512 helix: 2.58 (0.07), residues: 5379 sheet: -0.46 (0.14), residues: 1327 loop : -2.69 (0.07), residues: 5806 =============================================================================== Job complete usr+sys time: 30753.82 seconds wall clock time: 536 minutes 7.11 seconds (32167.11 seconds total)