Starting phenix.real_space_refine on Sun Feb 18 19:30:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8der_27396/02_2024/8der_27396.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8der_27396/02_2024/8der_27396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8der_27396/02_2024/8der_27396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8der_27396/02_2024/8der_27396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8der_27396/02_2024/8der_27396.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8der_27396/02_2024/8der_27396.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 14269 2.51 5 N 3899 2.21 5 O 4362 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "X PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 85": "OE1" <-> "OE2" Residue "X TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 113": "OD1" <-> "OD2" Residue "G PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 345": "OE1" <-> "OE2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "E PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 117": "OD1" <-> "OD2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 202": "OD1" <-> "OD2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C GLU 76": "OE1" <-> "OE2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "F PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 188": "OD1" <-> "OD2" Residue "F PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 34": "OE1" <-> "OE2" Residue "B TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 263": "OD1" <-> "OD2" Residue "B PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 83": "OE1" <-> "OE2" Residue "V TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "V TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22665 Number of models: 1 Model: "" Number of chains: 18 Chain: "X" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "Y" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "G" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3068 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 373} Chain: "E" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3068 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 373} Chain: "C" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2707 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 320} Chain: "F" Number of atoms: 3068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3068 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 373} Chain: "B" Number of atoms: 2707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2707 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 24, 'TRANS': 320} Chain: "A" Number of atoms: 2699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2699 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 23, 'TRANS': 320} Chain: "H" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "W" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 949 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "V" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 788 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 97} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 12.13, per 1000 atoms: 0.54 Number of scatterers: 22665 At special positions: 0 Unit cell: (169.32, 165.585, 158.115, 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 135 16.00 O 4362 8.00 N 3899 7.00 C 14269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS X 22 " - pdb=" SG CYS X 92 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.03 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.04 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.04 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS E 49 " - pdb=" SG CYS E 114 " distance=2.03 Simple disulfide: pdb=" SG CYS E 62 " - pdb=" SG CYS E 94 " distance=2.03 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 259 " - pdb=" SG CYS E 271 " distance=2.03 Simple disulfide: pdb=" SG CYS E 301 " - pdb=" SG CYS E 376 " distance=2.04 Simple disulfide: pdb=" SG CYS E 306 " - pdb=" SG CYS E 380 " distance=2.03 Simple disulfide: pdb=" SG CYS E 328 " - pdb=" SG CYS E 370 " distance=2.02 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 27 " distance=2.03 Simple disulfide: pdb=" SG CYS C 90 " - pdb=" SG CYS C 104 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 266 " distance=2.04 Simple disulfide: pdb=" SG CYS C 200 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS C 202 " - pdb=" SG CYS C 220 " distance=2.03 Simple disulfide: pdb=" SG CYS F 49 " - pdb=" SG CYS F 114 " distance=2.03 Simple disulfide: pdb=" SG CYS F 62 " - pdb=" SG CYS F 94 " distance=2.02 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 96 " distance=2.05 Simple disulfide: pdb=" SG CYS F 259 " - pdb=" SG CYS F 271 " distance=2.03 Simple disulfide: pdb=" SG CYS F 301 " - pdb=" SG CYS F 376 " distance=2.03 Simple disulfide: pdb=" SG CYS F 306 " - pdb=" SG CYS F 380 " distance=2.03 Simple disulfide: pdb=" SG CYS F 328 " - pdb=" SG CYS F 370 " distance=2.02 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 27 " distance=2.03 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 266 " distance=2.03 Simple disulfide: pdb=" SG CYS B 200 " - pdb=" SG CYS B 226 " distance=2.03 Simple disulfide: pdb=" SG CYS B 202 " - pdb=" SG CYS B 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 27 " distance=2.03 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 104 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 200 " - pdb=" SG CYS A 226 " distance=2.02 Simple disulfide: pdb=" SG CYS A 202 " - pdb=" SG CYS A 220 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS W 22 " - pdb=" SG CYS W 92 " distance=2.06 Simple disulfide: pdb=" SG CYS V 23 " - pdb=" SG CYS V 88 " distance=2.03 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG D 1 " - " ASN C 212 " " NAG E 501 " - " ASN E 134 " " NAG F 501 " - " ASN F 134 " " NAG G 501 " - " ASN G 134 " " NAG I 1 " - " ASN B 212 " " NAG J 1 " - " ASN A 212 " Time building additional restraints: 8.21 Conformation dependent library (CDL) restraints added in 4.3 seconds 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5386 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 79 sheets defined 6.3% alpha, 46.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.86 Creating SS restraints... Processing helix chain 'X' and resid 28 through 32 removed outlier: 3.550A pdb=" N PHE X 32 " --> pdb=" O PHE X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 87 Processing helix chain 'Y' and resid 79 through 83 Processing helix chain 'G' and resid 112 through 116 removed outlier: 4.393A pdb=" N LEU G 115 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 159 removed outlier: 3.731A pdb=" N VAL G 159 " --> pdb=" O PHE G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 254 Processing helix chain 'G' and resid 255 through 259 removed outlier: 3.912A pdb=" N GLY G 258 " --> pdb=" O ALA G 255 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS G 259 " --> pdb=" O PRO G 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 255 through 259' Processing helix chain 'G' and resid 283 through 287 removed outlier: 3.667A pdb=" N PHE G 287 " --> pdb=" O ASP G 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 247 Processing helix chain 'E' and resid 250 through 255 Processing helix chain 'E' and resid 256 through 259 Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.695A pdb=" N PHE C 6 " --> pdb=" O THR C 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 6' Processing helix chain 'C' and resid 80 through 82 No H-bonds generated for 'chain 'C' and resid 80 through 82' Processing helix chain 'C' and resid 202 through 205 Processing helix chain 'C' and resid 222 through 224 No H-bonds generated for 'chain 'C' and resid 222 through 224' Processing helix chain 'F' and resid 238 through 247 Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 256 through 259 Processing helix chain 'F' and resid 283 through 287 removed outlier: 4.022A pdb=" N PHE F 287 " --> pdb=" O ASP F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 293 Processing helix chain 'B' and resid 1 through 6 removed outlier: 4.021A pdb=" N GLU B 4 " --> pdb=" O SER B 1 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 12 Processing helix chain 'B' and resid 80 through 82 No H-bonds generated for 'chain 'B' and resid 80 through 82' Processing helix chain 'B' and resid 222 through 224 No H-bonds generated for 'chain 'B' and resid 222 through 224' Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.759A pdb=" N PHE A 6 " --> pdb=" O THR A 2 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2 through 7' Processing helix chain 'A' and resid 8 through 12 Processing helix chain 'A' and resid 222 through 224 No H-bonds generated for 'chain 'A' and resid 222 through 224' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.630A pdb=" N PHE H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'W' and resid 28 through 32 removed outlier: 3.968A pdb=" N ASP W 31 " --> pdb=" O ARG W 28 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE W 32 " --> pdb=" O PHE W 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 28 through 32' Processing helix chain 'W' and resid 61 through 64 Processing helix chain 'W' and resid 83 through 87 Processing helix chain 'V' and resid 27 through 31 Processing helix chain 'V' and resid 79 through 83 removed outlier: 3.775A pdb=" N GLU V 83 " --> pdb=" O ALA V 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'X' and resid 10 through 12 removed outlier: 6.715A pdb=" N MET X 34 " --> pdb=" O ARG X 50 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 10 through 12 removed outlier: 6.762A pdb=" N CYS X 92 " --> pdb=" O TRP X 103 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N TRP X 103 " --> pdb=" O CYS X 92 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG X 94 " --> pdb=" O ASP X 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Y' and resid 9 through 12 removed outlier: 5.845A pdb=" N GLN Y 37 " --> pdb=" O LEU Y 46 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU Y 46 " --> pdb=" O GLN Y 37 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Y' and resid 9 through 12 Processing sheet with id=AA6, first strand: chain 'Y' and resid 19 through 24 Processing sheet with id=AA7, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AA8, first strand: chain 'G' and resid 15 through 21 removed outlier: 5.381A pdb=" N ARG G 21 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE G 31 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN G 134 " --> pdb=" O PRO G 33 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS G 35 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL G 47 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 140 through 148 removed outlier: 4.340A pdb=" N VAL G 129 " --> pdb=" O VAL G 148 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU G 120 " --> pdb=" O VAL G 47 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL G 47 " --> pdb=" O GLU G 120 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N TYR G 122 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLU G 45 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ALA G 124 " --> pdb=" O ASN G 43 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N ASN G 43 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR G 126 " --> pdb=" O THR G 41 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS G 35 " --> pdb=" O PHE G 132 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN G 134 " --> pdb=" O PRO G 33 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N THR G 136 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE G 31 " --> pdb=" O THR G 136 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 51 through 55 Processing sheet with id=AB2, first strand: chain 'G' and resid 51 through 55 Processing sheet with id=AB3, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AB4, first strand: chain 'G' and resid 203 through 204 removed outlier: 3.548A pdb=" N TYR G 214 " --> pdb=" O GLN G 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AB6, first strand: chain 'G' and resid 296 through 305 removed outlier: 6.328A pdb=" N ALA G 299 " --> pdb=" O SER G 321 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER G 321 " --> pdb=" O ALA G 299 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N CYS G 301 " --> pdb=" O LYS G 319 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS G 319 " --> pdb=" O CYS G 301 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU G 303 " --> pdb=" O THR G 317 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N THR G 317 " --> pdb=" O LEU G 303 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 343 through 346 Processing sheet with id=AB8, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AB9, first strand: chain 'E' and resid 2 through 4 Processing sheet with id=AC1, first strand: chain 'E' and resid 7 through 8 Processing sheet with id=AC2, first strand: chain 'E' and resid 15 through 19 removed outlier: 5.415A pdb=" N ILE E 31 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN E 134 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR E 126 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASN E 43 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLU E 45 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 47 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 140 through 148 removed outlier: 4.391A pdb=" N VAL E 129 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLU E 120 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL E 47 " --> pdb=" O GLU E 120 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N TYR E 122 " --> pdb=" O GLU E 45 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLU E 45 " --> pdb=" O TYR E 122 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ALA E 124 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N ASN E 43 " --> pdb=" O ALA E 124 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N THR E 126 " --> pdb=" O THR E 41 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASN E 134 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N THR E 136 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE E 31 " --> pdb=" O THR E 136 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 51 through 55 Processing sheet with id=AC5, first strand: chain 'E' and resid 51 through 55 Processing sheet with id=AC6, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AC7, first strand: chain 'E' and resid 203 through 204 Processing sheet with id=AC8, first strand: chain 'E' and resid 220 through 221 Processing sheet with id=AC9, first strand: chain 'E' and resid 297 through 306 removed outlier: 5.971A pdb=" N ALA E 299 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N SER E 321 " --> pdb=" O ALA E 299 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N CYS E 301 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS E 319 " --> pdb=" O CYS E 301 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N LEU E 303 " --> pdb=" O THR E 317 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N THR E 317 " --> pdb=" O LEU E 303 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 343 through 346 Processing sheet with id=AD2, first strand: chain 'E' and resid 387 through 388 Processing sheet with id=AD3, first strand: chain 'C' and resid 17 through 19 Processing sheet with id=AD4, first strand: chain 'C' and resid 33 through 40 removed outlier: 8.295A pdb=" N ILE C 33 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER C 50 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C 35 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP C 39 " --> pdb=" O TYR C 44 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N TYR C 44 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 9.532A pdb=" N SER C 50 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ASP C 69 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N THR C 65 " --> pdb=" O GLY C 54 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 33 through 40 removed outlier: 8.295A pdb=" N ILE C 33 " --> pdb=" O SER C 50 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER C 50 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA C 35 " --> pdb=" O GLN C 48 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP C 39 " --> pdb=" O TYR C 44 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N TYR C 44 " --> pdb=" O ASP C 39 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N TYR C 98 " --> pdb=" O THR C 49 " (cutoff:3.500A) removed outlier: 9.661A pdb=" N SER C 51 " --> pdb=" O HIS C 96 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N HIS C 96 " --> pdb=" O SER C 51 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N TYR C 53 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 10.495A pdb=" N ASP C 94 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 14.232A pdb=" N LEU C 55 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 16.997A pdb=" N ILE C 92 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AD7, first strand: chain 'C' and resid 147 through 154 Processing sheet with id=AD8, first strand: chain 'C' and resid 237 through 238 Processing sheet with id=AD9, first strand: chain 'C' and resid 173 through 174 removed outlier: 3.583A pdb=" N GLU C 173 " --> pdb=" O ARG C 230 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 179 through 181 Processing sheet with id=AE2, first strand: chain 'C' and resid 275 through 279 Processing sheet with id=AE3, first strand: chain 'F' and resid 2 through 8 Processing sheet with id=AE4, first strand: chain 'F' and resid 15 through 21 removed outlier: 3.831A pdb=" N LEU F 27 " --> pdb=" O VAL F 19 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ARG F 21 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA F 25 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE F 31 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR F 136 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN F 134 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR F 126 " --> pdb=" O THR F 41 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN F 43 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA F 124 " --> pdb=" O ASN F 43 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU F 45 " --> pdb=" O TYR F 122 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR F 122 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL F 47 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N GLU F 120 " --> pdb=" O VAL F 47 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 143 through 147 removed outlier: 6.816A pdb=" N GLU F 120 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL F 47 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N TYR F 122 " --> pdb=" O GLU F 45 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N GLU F 45 " --> pdb=" O TYR F 122 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ALA F 124 " --> pdb=" O ASN F 43 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ASN F 43 " --> pdb=" O ALA F 124 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR F 126 " --> pdb=" O THR F 41 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN F 134 " --> pdb=" O PRO F 33 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N THR F 136 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE F 31 " --> pdb=" O THR F 136 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 51 through 61 removed outlier: 4.678A pdb=" N LYS F 105 " --> pdb=" O ASP F 56 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N VAL F 103 " --> pdb=" O PRO F 58 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ILE F 60 " --> pdb=" O THR F 101 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N THR F 101 " --> pdb=" O ILE F 60 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=AE8, first strand: chain 'F' and resid 203 through 205 Processing sheet with id=AE9, first strand: chain 'F' and resid 220 through 221 Processing sheet with id=AF1, first strand: chain 'F' and resid 300 through 306 removed outlier: 6.518A pdb=" N ILE F 315 " --> pdb=" O ASN F 304 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 326 through 329 removed outlier: 3.524A pdb=" N CYS F 328 " --> pdb=" O VAL F 344 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 364 through 368 Processing sheet with id=AF4, first strand: chain 'F' and resid 387 through 388 Processing sheet with id=AF5, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AF6, first strand: chain 'B' and resid 33 through 37 removed outlier: 8.517A pdb=" N ILE B 33 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER B 50 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 9.574A pdb=" N SER B 50 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ASP B 69 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR B 65 " --> pdb=" O GLY B 54 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 33 through 37 removed outlier: 8.517A pdb=" N ILE B 33 " --> pdb=" O SER B 50 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N SER B 50 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N TYR B 98 " --> pdb=" O THR B 49 " (cutoff:3.500A) removed outlier: 9.662A pdb=" N SER B 51 " --> pdb=" O HIS B 96 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N HIS B 96 " --> pdb=" O SER B 51 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N TYR B 53 " --> pdb=" O ASP B 94 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N ASP B 94 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 14.595A pdb=" N LEU B 55 " --> pdb=" O ILE B 92 " (cutoff:3.500A) removed outlier: 17.227A pdb=" N ILE B 92 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 83 through 85 Processing sheet with id=AF9, first strand: chain 'B' and resid 147 through 154 Processing sheet with id=AG1, first strand: chain 'B' and resid 237 through 238 removed outlier: 3.821A pdb=" N GLY B 253 " --> pdb=" O MET B 167 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 173 through 174 removed outlier: 3.878A pdb=" N GLU B 173 " --> pdb=" O ARG B 230 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 195 " --> pdb=" O LEU B 231 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N CYS B 202 " --> pdb=" O THR B 205 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 179 through 182 removed outlier: 3.952A pdb=" N VAL B 186 " --> pdb=" O PHE B 217 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 275 through 279 Processing sheet with id=AG5, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AG6, first strand: chain 'A' and resid 33 through 37 removed outlier: 3.590A pdb=" N ALA A 35 " --> pdb=" O GLN A 48 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE A 99 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLY A 95 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU A 101 " --> pdb=" O VAL A 93 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'A' and resid 65 through 70 Processing sheet with id=AG8, first strand: chain 'A' and resid 82 through 85 Processing sheet with id=AG9, first strand: chain 'A' and resid 147 through 154 Processing sheet with id=AH1, first strand: chain 'A' and resid 237 through 238 Processing sheet with id=AH2, first strand: chain 'A' and resid 173 through 174 removed outlier: 3.997A pdb=" N GLU A 173 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 195 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.882A pdb=" N VAL A 186 " --> pdb=" O PHE A 217 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 275 through 279 Processing sheet with id=AH5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AH6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.346A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.715A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.534A pdb=" N VAL L 11 " --> pdb=" O ARG L 103 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.534A pdb=" N VAL L 11 " --> pdb=" O ARG L 103 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AI2, first strand: chain 'W' and resid 3 through 7 Processing sheet with id=AI3, first strand: chain 'W' and resid 11 through 12 removed outlier: 6.656A pdb=" N MET W 34 " --> pdb=" O ARG W 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG W 50 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP W 36 " --> pdb=" O VAL W 48 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'W' and resid 11 through 12 removed outlier: 6.555A pdb=" N CYS W 92 " --> pdb=" O TRP W 103 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TRP W 103 " --> pdb=" O CYS W 92 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG W 94 " --> pdb=" O ASP W 101 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'V' and resid 9 through 12 removed outlier: 6.293A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TRP V 35 " --> pdb=" O VAL V 47 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'V' and resid 9 through 12 removed outlier: 6.293A pdb=" N VAL V 11 " --> pdb=" O THR V 105 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 19 through 24 839 hydrogen bonds defined for protein. 1992 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.29 Time building geometry restraints manager: 8.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7364 1.34 - 1.47: 5729 1.47 - 1.59: 9997 1.59 - 1.72: 0 1.72 - 1.85: 174 Bond restraints: 23264 Sorted by residual: bond pdb=" N PRO F 333 " pdb=" CD PRO F 333 " ideal model delta sigma weight residual 1.473 1.421 0.052 1.40e-02 5.10e+03 1.36e+01 bond pdb=" N CYS F 328 " pdb=" CA CYS F 328 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.26e-02 6.30e+03 1.02e+01 bond pdb=" N GLN F 349 " pdb=" CA GLN F 349 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.08e-02 8.57e+03 9.84e+00 bond pdb=" CA SER W 100C" pdb=" CB SER W 100C" ideal model delta sigma weight residual 1.534 1.478 0.056 1.78e-02 3.16e+03 9.82e+00 bond pdb=" N VAL C 119 " pdb=" CA VAL C 119 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.29e-02 6.01e+03 9.60e+00 ... (remaining 23259 not shown) Histogram of bond angle deviations from ideal: 98.31 - 105.54: 691 105.54 - 112.77: 12205 112.77 - 120.00: 8107 120.00 - 127.23: 10298 127.23 - 134.46: 362 Bond angle restraints: 31663 Sorted by residual: angle pdb=" C THR F 371 " pdb=" N SER F 372 " pdb=" CA SER F 372 " ideal model delta sigma weight residual 122.53 112.54 9.99 1.61e+00 3.86e-01 3.85e+01 angle pdb=" N PRO W 97 " pdb=" CA PRO W 97 " pdb=" C PRO W 97 " ideal model delta sigma weight residual 113.53 105.83 7.70 1.39e+00 5.18e-01 3.07e+01 angle pdb=" N ILE F 361 " pdb=" CA ILE F 361 " pdb=" C ILE F 361 " ideal model delta sigma weight residual 110.62 105.57 5.05 1.02e+00 9.61e-01 2.45e+01 angle pdb=" N ASN C 212 " pdb=" CA ASN C 212 " pdb=" C ASN C 212 " ideal model delta sigma weight residual 113.30 106.94 6.36 1.34e+00 5.57e-01 2.25e+01 angle pdb=" CA GLY W 106 " pdb=" C GLY W 106 " pdb=" O GLY W 106 " ideal model delta sigma weight residual 121.88 118.24 3.64 7.80e-01 1.64e+00 2.17e+01 ... (remaining 31658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.21: 13270 21.21 - 42.42: 675 42.42 - 63.63: 91 63.63 - 84.84: 31 84.84 - 106.04: 6 Dihedral angle restraints: 14073 sinusoidal: 5640 harmonic: 8433 Sorted by residual: dihedral pdb=" CB CYS E 328 " pdb=" SG CYS E 328 " pdb=" SG CYS E 370 " pdb=" CB CYS E 370 " ideal model delta sinusoidal sigma weight residual 93.00 151.18 -58.18 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CB CYS G 63 " pdb=" SG CYS G 63 " pdb=" SG CYS G 96 " pdb=" CB CYS G 96 " ideal model delta sinusoidal sigma weight residual 93.00 44.29 48.71 1 1.00e+01 1.00e-02 3.27e+01 dihedral pdb=" CB CYS E 301 " pdb=" SG CYS E 301 " pdb=" SG CYS E 376 " pdb=" CB CYS E 376 " ideal model delta sinusoidal sigma weight residual -86.00 -38.42 -47.58 1 1.00e+01 1.00e-02 3.12e+01 ... (remaining 14070 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 3398 0.133 - 0.267: 85 0.267 - 0.400: 5 0.400 - 0.533: 1 0.533 - 0.667: 1 Chirality restraints: 3490 Sorted by residual: chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-02 2.50e+03 1.95e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.29 -0.11 2.00e-02 2.50e+03 3.25e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 212 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-01 2.50e+01 1.11e+01 ... (remaining 3487 not shown) Planarity restraints: 4110 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 501 " -0.326 2.00e-02 2.50e+03 2.76e-01 9.52e+02 pdb=" C7 NAG G 501 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG G 501 " -0.187 2.00e-02 2.50e+03 pdb=" N2 NAG G 501 " 0.479 2.00e-02 2.50e+03 pdb=" O7 NAG G 501 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 501 " -0.316 2.00e-02 2.50e+03 2.69e-01 9.06e+02 pdb=" C7 NAG E 501 " 0.081 2.00e-02 2.50e+03 pdb=" C8 NAG E 501 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG E 501 " 0.469 2.00e-02 2.50e+03 pdb=" O7 NAG E 501 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.213 2.00e-02 2.50e+03 1.76e-01 3.89e+02 pdb=" C7 NAG I 1 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.289 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.018 2.00e-02 2.50e+03 ... (remaining 4107 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 138 2.55 - 3.14: 17778 3.14 - 3.73: 32978 3.73 - 4.31: 47899 4.31 - 4.90: 82124 Nonbonded interactions: 180917 Sorted by model distance: nonbonded pdb=" OG1 THR B 297 " pdb=" OG1 THR B 307 " model vdw 1.967 2.440 nonbonded pdb=" O SER G 297 " pdb=" OG SER G 321 " model vdw 1.996 2.440 nonbonded pdb=" OG1 THR A 277 " pdb=" OG SER A 284 " model vdw 2.016 2.440 nonbonded pdb=" OE1 GLN F 179 " pdb=" OG1 THR F 263 " model vdw 2.044 2.440 nonbonded pdb=" OG1 THR A 297 " pdb=" OG1 THR A 307 " model vdw 2.061 2.440 ... (remaining 180912 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' and resid 1 through 344) selection = (chain 'C' and resid 1 through 344) } ncs_group { reference = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'L' selection = chain 'V' selection = chain 'Y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.770 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 59.610 Find NCS groups from input model: 1.440 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 23264 Z= 0.345 Angle : 0.849 11.665 31663 Z= 0.498 Chirality : 0.057 0.667 3490 Planarity : 0.010 0.276 4104 Dihedral : 12.829 106.045 8552 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: -0.74 (0.15), residues: 2897 helix: -2.61 (0.56), residues: 66 sheet: -0.26 (0.15), residues: 1151 loop : -0.50 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP W 103 HIS 0.008 0.001 HIS C 141 PHE 0.036 0.002 PHE X 67 TYR 0.029 0.002 TYR G 15 ARG 0.016 0.001 ARG F 223 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 663 time to evaluate : 2.679 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 47 TRP cc_start: 0.7165 (t60) cc_final: 0.6705 (t60) REVERT: X 100 TYR cc_start: 0.7693 (t80) cc_final: 0.7459 (t80) REVERT: X 100 HIS cc_start: 0.7138 (m90) cc_final: 0.6911 (m-70) REVERT: G 72 TYR cc_start: 0.6578 (m-10) cc_final: 0.6370 (m-80) REVERT: G 142 ILE cc_start: 0.7969 (pt) cc_final: 0.7689 (mt) REVERT: G 202 ASP cc_start: 0.7876 (p0) cc_final: 0.7494 (p0) REVERT: G 246 ASP cc_start: 0.6845 (m-30) cc_final: 0.6521 (m-30) REVERT: E 128 SER cc_start: 0.8456 (t) cc_final: 0.8143 (p) REVERT: E 202 ASP cc_start: 0.7858 (p0) cc_final: 0.7657 (p0) REVERT: E 304 ASN cc_start: 0.7050 (m110) cc_final: 0.6516 (m110) REVERT: E 311 ASP cc_start: 0.6734 (p0) cc_final: 0.6386 (p0) REVERT: E 319 LYS cc_start: 0.8250 (mmmt) cc_final: 0.7968 (mmmt) REVERT: C 3 GLU cc_start: 0.7775 (tp30) cc_final: 0.7569 (tp30) REVERT: C 53 TYR cc_start: 0.8473 (m-80) cc_final: 0.7945 (m-80) REVERT: C 70 MET cc_start: 0.7890 (tpp) cc_final: 0.7563 (tpt) REVERT: C 112 MET cc_start: 0.7984 (ttm) cc_final: 0.7726 (ttt) REVERT: C 313 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6703 (mt-10) REVERT: F 29 ILE cc_start: 0.8265 (mt) cc_final: 0.8046 (mt) REVERT: F 186 ASN cc_start: 0.8514 (m-40) cc_final: 0.7923 (m-40) REVERT: F 319 LYS cc_start: 0.8572 (mtpp) cc_final: 0.8371 (mtpp) REVERT: F 341 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7166 (mt-10) REVERT: F 353 THR cc_start: 0.8161 (p) cc_final: 0.7913 (p) REVERT: F 356 PHE cc_start: 0.7748 (p90) cc_final: 0.7546 (p90) REVERT: F 402 VAL cc_start: 0.3867 (p) cc_final: 0.2594 (m) REVERT: B 53 TYR cc_start: 0.8156 (m-80) cc_final: 0.7866 (m-80) REVERT: B 84 LEU cc_start: 0.8064 (pt) cc_final: 0.7801 (pp) REVERT: B 112 MET cc_start: 0.8419 (ttt) cc_final: 0.8109 (ttp) REVERT: B 130 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7994 (mtpp) REVERT: B 137 GLU cc_start: 0.6585 (mt-10) cc_final: 0.6375 (mt-10) REVERT: B 148 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6931 (mm-30) REVERT: B 161 ARG cc_start: 0.7665 (tpp80) cc_final: 0.7049 (mmt90) REVERT: B 238 TYR cc_start: 0.7526 (t80) cc_final: 0.7034 (t80) REVERT: B 275 MET cc_start: 0.7218 (mtm) cc_final: 0.7007 (mtp) REVERT: B 282 SER cc_start: 0.8338 (t) cc_final: 0.8079 (p) REVERT: B 332 ASN cc_start: 0.8461 (m-40) cc_final: 0.7778 (m110) REVERT: A 8 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7347 (mt-10) REVERT: A 57 SER cc_start: 0.8436 (m) cc_final: 0.8080 (t) REVERT: A 88 ARG cc_start: 0.8255 (mtm-85) cc_final: 0.7914 (mtp180) REVERT: A 224 GLU cc_start: 0.7592 (tp30) cc_final: 0.7330 (tp30) REVERT: A 254 LYS cc_start: 0.7714 (mttp) cc_final: 0.6993 (mtmm) REVERT: A 276 ILE cc_start: 0.8913 (mm) cc_final: 0.8541 (mm) REVERT: W 100 TYR cc_start: 0.7989 (t80) cc_final: 0.7682 (t80) REVERT: V 54 ARG cc_start: 0.7563 (mtt-85) cc_final: 0.6979 (mtt-85) outliers start: 0 outliers final: 0 residues processed: 663 average time/residue: 0.3516 time to fit residues: 356.6653 Evaluate side-chains 605 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 605 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 243 optimal weight: 1.9990 chunk 218 optimal weight: 2.9990 chunk 121 optimal weight: 0.0670 chunk 74 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 116 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 261 optimal weight: 9.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN G 196 GLN G 204 GLN G 222 GLN G 304 ASN E 20 ASN E 118 HIS E 218 ASN E 270 ASN E 362 HIS E 392 GLN E 396 GLN C 141 HIS C 305 HIS ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 16 ASN F 204 GLN F 355 HIS F 362 HIS ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 288 HIS A 132 ASN A 159 GLN ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 299 GLN H 33 HIS W 100DHIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23264 Z= 0.222 Angle : 0.630 7.092 31663 Z= 0.327 Chirality : 0.046 0.247 3490 Planarity : 0.005 0.052 4104 Dihedral : 6.824 65.015 3392 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.91 % Allowed : 10.06 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 2897 helix: -2.66 (0.51), residues: 66 sheet: -0.03 (0.15), residues: 1083 loop : -0.52 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 99 HIS 0.008 0.001 HIS H 52A PHE 0.023 0.002 PHE G 365 TYR 0.018 0.001 TYR G 122 ARG 0.005 0.000 ARG F 267 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 617 time to evaluate : 2.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: X 47 TRP cc_start: 0.7251 (t60) cc_final: 0.6635 (t60) REVERT: Y 73 LEU cc_start: 0.6812 (tp) cc_final: 0.6431 (tp) REVERT: G 142 ILE cc_start: 0.7901 (pt) cc_final: 0.7666 (mt) REVERT: G 202 ASP cc_start: 0.7758 (p0) cc_final: 0.7434 (p0) REVERT: G 220 VAL cc_start: 0.8399 (p) cc_final: 0.8032 (t) REVERT: G 246 ASP cc_start: 0.6892 (m-30) cc_final: 0.6546 (m-30) REVERT: E 1 TYR cc_start: 0.7194 (t80) cc_final: 0.6911 (t80) REVERT: E 94 CYS cc_start: 0.5755 (m) cc_final: 0.5320 (m) REVERT: E 114 CYS cc_start: 0.5743 (t) cc_final: 0.5215 (t) REVERT: E 304 ASN cc_start: 0.7050 (m110) cc_final: 0.6615 (m110) REVERT: E 311 ASP cc_start: 0.6884 (p0) cc_final: 0.6598 (p0) REVERT: C 3 GLU cc_start: 0.7787 (tp30) cc_final: 0.7572 (tp30) REVERT: C 42 ASP cc_start: 0.6604 (p0) cc_final: 0.6089 (p0) REVERT: C 53 TYR cc_start: 0.8374 (m-80) cc_final: 0.8074 (m-80) REVERT: C 70 MET cc_start: 0.7856 (tpp) cc_final: 0.7605 (tpt) REVERT: C 112 MET cc_start: 0.8098 (ttm) cc_final: 0.7670 (ttt) REVERT: C 313 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6758 (mt-10) REVERT: F 38 LEU cc_start: 0.7328 (tp) cc_final: 0.7120 (tt) REVERT: F 45 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7234 (mm-30) REVERT: F 174 ASP cc_start: 0.6974 (p0) cc_final: 0.6586 (p0) REVERT: F 186 ASN cc_start: 0.8505 (m-40) cc_final: 0.7322 (m-40) REVERT: F 315 ILE cc_start: 0.7711 (mp) cc_final: 0.7442 (mm) REVERT: F 353 THR cc_start: 0.8238 (p) cc_final: 0.8023 (p) REVERT: F 402 VAL cc_start: 0.4316 (p) cc_final: 0.2982 (m) REVERT: B 49 THR cc_start: 0.8254 (m) cc_final: 0.7941 (p) REVERT: B 53 TYR cc_start: 0.8212 (m-80) cc_final: 0.7867 (m-80) REVERT: B 112 MET cc_start: 0.8450 (ttt) cc_final: 0.8152 (ttp) REVERT: B 130 LYS cc_start: 0.8325 (mtmm) cc_final: 0.8022 (mtpp) REVERT: B 148 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6947 (mm-30) REVERT: B 154 TYR cc_start: 0.8598 (m-80) cc_final: 0.8310 (m-80) REVERT: B 157 ASP cc_start: 0.7347 (t0) cc_final: 0.7104 (t0) REVERT: B 231 LEU cc_start: 0.8749 (tp) cc_final: 0.8479 (tt) REVERT: B 275 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.7028 (mtp) REVERT: A 57 SER cc_start: 0.8478 (m) cc_final: 0.8096 (t) REVERT: A 254 LYS cc_start: 0.7701 (mttp) cc_final: 0.7199 (tttp) REVERT: A 276 ILE cc_start: 0.8907 (mm) cc_final: 0.8443 (mm) REVERT: H 31 ASP cc_start: 0.7021 (m-30) cc_final: 0.6766 (m-30) REVERT: H 76 ASN cc_start: 0.8380 (t0) cc_final: 0.8067 (t0) REVERT: W 59 PHE cc_start: 0.7343 (m-80) cc_final: 0.6761 (m-80) REVERT: V 2 MET cc_start: 0.4386 (tpp) cc_final: 0.4009 (tpt) REVERT: V 54 ARG cc_start: 0.7623 (mtt-85) cc_final: 0.7238 (mtt-85) outliers start: 47 outliers final: 29 residues processed: 627 average time/residue: 0.3458 time to fit residues: 332.5813 Evaluate side-chains 621 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 591 time to evaluate : 2.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 222 GLN Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain E residue 396 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 145 optimal weight: 0.6980 chunk 81 optimal weight: 0.0970 chunk 217 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 262 optimal weight: 1.9990 chunk 283 optimal weight: 0.2980 chunk 233 optimal weight: 3.9990 chunk 259 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 GLN ** G 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 392 GLN C 141 HIS C 288 HIS C 341 GLN ** F 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 157 ASN F 204 GLN F 235 GLN F 349 GLN F 355 HIS ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 288 HIS A 132 ASN A 288 HIS A 299 GLN A 332 ASN W 100DHIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23264 Z= 0.238 Angle : 0.606 9.323 31663 Z= 0.314 Chirality : 0.045 0.280 3490 Planarity : 0.005 0.049 4104 Dihedral : 6.174 53.065 3392 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.89 % Allowed : 12.05 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: -0.58 (0.15), residues: 2897 helix: -2.56 (0.53), residues: 66 sheet: 0.01 (0.15), residues: 1103 loop : -0.51 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP X 99 HIS 0.008 0.001 HIS C 141 PHE 0.029 0.002 PHE F 365 TYR 0.021 0.001 TYR G 320 ARG 0.005 0.000 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 592 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 73 LEU cc_start: 0.6765 (tp) cc_final: 0.6357 (tp) REVERT: G 38 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7945 (tp) REVERT: G 55 MET cc_start: 0.8315 (ptp) cc_final: 0.8098 (mtm) REVERT: G 142 ILE cc_start: 0.7913 (pt) cc_final: 0.7673 (mt) REVERT: G 166 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7762 (mt) REVERT: G 202 ASP cc_start: 0.7750 (p0) cc_final: 0.7450 (p0) REVERT: G 220 VAL cc_start: 0.8377 (p) cc_final: 0.7824 (t) REVERT: G 246 ASP cc_start: 0.6906 (m-30) cc_final: 0.6535 (m-30) REVERT: G 402 VAL cc_start: 0.3365 (OUTLIER) cc_final: 0.2062 (t) REVERT: E 1 TYR cc_start: 0.7113 (t80) cc_final: 0.6830 (t80) REVERT: E 94 CYS cc_start: 0.5843 (m) cc_final: 0.5406 (m) REVERT: E 304 ASN cc_start: 0.7137 (m110) cc_final: 0.6597 (m110) REVERT: E 311 ASP cc_start: 0.6902 (p0) cc_final: 0.6565 (p0) REVERT: E 319 LYS cc_start: 0.8109 (mmmt) cc_final: 0.7734 (mmmt) REVERT: E 327 LYS cc_start: 0.7572 (mmmm) cc_final: 0.7333 (mmmm) REVERT: C 3 GLU cc_start: 0.7801 (tp30) cc_final: 0.7568 (tp30) REVERT: C 42 ASP cc_start: 0.6610 (p0) cc_final: 0.6252 (p0) REVERT: C 53 TYR cc_start: 0.8378 (m-80) cc_final: 0.8175 (m-80) REVERT: C 70 MET cc_start: 0.7781 (tpp) cc_final: 0.7564 (tpt) REVERT: C 205 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8061 (p) REVERT: C 313 GLU cc_start: 0.7068 (mt-10) cc_final: 0.6797 (mt-10) REVERT: F 45 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7070 (mm-30) REVERT: F 75 ASP cc_start: 0.7878 (t70) cc_final: 0.7675 (t0) REVERT: F 157 ASN cc_start: 0.7275 (OUTLIER) cc_final: 0.6869 (t0) REVERT: F 309 SER cc_start: 0.7012 (t) cc_final: 0.6733 (p) REVERT: F 315 ILE cc_start: 0.7722 (mp) cc_final: 0.7461 (mm) REVERT: F 402 VAL cc_start: 0.4326 (p) cc_final: 0.2987 (m) REVERT: B 49 THR cc_start: 0.8221 (m) cc_final: 0.7704 (p) REVERT: B 53 TYR cc_start: 0.8177 (m-80) cc_final: 0.7191 (m-80) REVERT: B 66 MET cc_start: 0.7538 (ttm) cc_final: 0.7079 (ttp) REVERT: B 68 TYR cc_start: 0.8589 (p90) cc_final: 0.8349 (p90) REVERT: B 112 MET cc_start: 0.8474 (ttt) cc_final: 0.8182 (ttp) REVERT: B 148 GLU cc_start: 0.7568 (mm-30) cc_final: 0.6944 (mm-30) REVERT: B 154 TYR cc_start: 0.8593 (m-80) cc_final: 0.8326 (m-80) REVERT: B 231 LEU cc_start: 0.8753 (tp) cc_final: 0.8496 (tt) REVERT: B 275 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6921 (mtp) REVERT: A 57 SER cc_start: 0.8473 (m) cc_final: 0.8102 (t) REVERT: A 62 LYS cc_start: 0.7986 (ttmm) cc_final: 0.7658 (mttt) REVERT: A 124 SER cc_start: 0.8221 (t) cc_final: 0.7599 (p) REVERT: A 276 ILE cc_start: 0.8902 (mm) cc_final: 0.8428 (mm) REVERT: H 31 ASP cc_start: 0.7072 (m-30) cc_final: 0.6755 (m-30) REVERT: H 76 ASN cc_start: 0.8306 (t0) cc_final: 0.8038 (t0) REVERT: W 59 PHE cc_start: 0.7323 (m-80) cc_final: 0.6821 (m-80) outliers start: 71 outliers final: 52 residues processed: 621 average time/residue: 0.3390 time to fit residues: 324.7346 Evaluate side-chains 640 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 582 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain A residue 65 THR Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 290 LYS Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain V residue 96 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 258 optimal weight: 10.0000 chunk 196 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 125 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 chunk 262 optimal weight: 6.9990 chunk 278 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 100DHIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 235 GLN G 304 ASN G 392 GLN ** E 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS F 204 GLN F 349 GLN F 355 HIS ** F 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 ASN B 288 HIS A 132 ASN A 332 ASN H 39 GLN L 37 GLN L 89 GLN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS V 37 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.107 23264 Z= 0.652 Angle : 0.774 11.677 31663 Z= 0.406 Chirality : 0.051 0.254 3490 Planarity : 0.006 0.054 4104 Dihedral : 6.677 65.520 3392 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.60 % Allowed : 13.72 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: -0.90 (0.15), residues: 2897 helix: -2.69 (0.51), residues: 66 sheet: -0.04 (0.15), residues: 1112 loop : -0.88 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP X 99 HIS 0.012 0.002 HIS H 52A PHE 0.034 0.003 PHE H 67 TYR 0.029 0.003 TYR X 91 ARG 0.006 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 642 time to evaluate : 2.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 38 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8001 (tp) REVERT: G 202 ASP cc_start: 0.7764 (p0) cc_final: 0.7551 (p0) REVERT: G 220 VAL cc_start: 0.8315 (p) cc_final: 0.7848 (t) REVERT: G 241 GLU cc_start: 0.6799 (tt0) cc_final: 0.6477 (tt0) REVERT: G 246 ASP cc_start: 0.6983 (m-30) cc_final: 0.6557 (m-30) REVERT: G 264 ASN cc_start: 0.7792 (m-40) cc_final: 0.7425 (m-40) REVERT: G 389 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8400 (t) REVERT: G 402 VAL cc_start: 0.3847 (OUTLIER) cc_final: 0.2525 (t) REVERT: E 15 TYR cc_start: 0.8470 (t80) cc_final: 0.8046 (t80) REVERT: E 94 CYS cc_start: 0.5907 (m) cc_final: 0.5309 (m) REVERT: E 114 CYS cc_start: 0.5829 (t) cc_final: 0.5251 (t) REVERT: E 157 ASN cc_start: 0.8559 (m-40) cc_final: 0.8334 (m-40) REVERT: E 304 ASN cc_start: 0.7235 (m110) cc_final: 0.6725 (m110) REVERT: E 311 ASP cc_start: 0.7046 (p0) cc_final: 0.6733 (p0) REVERT: E 319 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7738 (mmmt) REVERT: E 327 LYS cc_start: 0.7599 (mmmm) cc_final: 0.7350 (mmmm) REVERT: C 3 GLU cc_start: 0.7816 (tp30) cc_final: 0.7555 (tp30) REVERT: C 27 CYS cc_start: 0.5858 (p) cc_final: 0.5597 (p) REVERT: C 42 ASP cc_start: 0.6681 (p0) cc_final: 0.6368 (p0) REVERT: C 70 MET cc_start: 0.7735 (tpp) cc_final: 0.7515 (tpt) REVERT: C 108 ASP cc_start: 0.6975 (m-30) cc_final: 0.6756 (m-30) REVERT: C 313 GLU cc_start: 0.7103 (mt-10) cc_final: 0.6833 (mt-10) REVERT: F 45 GLU cc_start: 0.7335 (mm-30) cc_final: 0.7119 (mm-30) REVERT: F 98 THR cc_start: 0.7236 (t) cc_final: 0.7028 (t) REVERT: F 143 VAL cc_start: 0.7511 (OUTLIER) cc_final: 0.7286 (t) REVERT: F 260 GLU cc_start: 0.6483 (mt-10) cc_final: 0.6083 (mt-10) REVERT: F 309 SER cc_start: 0.7176 (t) cc_final: 0.6883 (p) REVERT: F 315 ILE cc_start: 0.7850 (mp) cc_final: 0.7575 (mm) REVERT: B 49 THR cc_start: 0.8261 (m) cc_final: 0.7893 (p) REVERT: B 130 LYS cc_start: 0.8411 (mtmm) cc_final: 0.8135 (mtpp) REVERT: B 148 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7064 (mm-30) REVERT: B 276 ILE cc_start: 0.8627 (mp) cc_final: 0.8341 (mt) REVERT: A 21 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7464 (mtp85) REVERT: A 48 GLN cc_start: 0.8219 (tt0) cc_final: 0.7767 (tt0) REVERT: A 57 SER cc_start: 0.8474 (m) cc_final: 0.8072 (t) REVERT: A 62 LYS cc_start: 0.7983 (ttmm) cc_final: 0.7651 (mttt) REVERT: A 124 SER cc_start: 0.8329 (t) cc_final: 0.7679 (p) REVERT: A 273 GLU cc_start: 0.7662 (pt0) cc_final: 0.7409 (pt0) REVERT: A 275 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6669 (mtm) REVERT: A 276 ILE cc_start: 0.8848 (mm) cc_final: 0.8447 (mm) REVERT: A 284 SER cc_start: 0.7818 (p) cc_final: 0.7584 (p) REVERT: H 31 ASP cc_start: 0.7017 (m-30) cc_final: 0.6760 (m-30) REVERT: W 59 PHE cc_start: 0.7185 (m-80) cc_final: 0.6661 (m-80) REVERT: W 82 MET cc_start: 0.6602 (mmm) cc_final: 0.6043 (mmm) REVERT: V 54 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.7284 (mtt-85) outliers start: 113 outliers final: 81 residues processed: 688 average time/residue: 0.3385 time to fit residues: 360.1743 Evaluate side-chains 687 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 600 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain X residue 96 SER Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 166 LEU Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 260 GLU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 362 HIS Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 34 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 295 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 346 LEU Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 212 ASN Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 329 VAL Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 39 GLN Chi-restraints excluded: chain H residue 52 HIS Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain W residue 100 SER Chi-restraints excluded: chain V residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 231 optimal weight: 0.5980 chunk 158 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 237 optimal weight: 0.6980 chunk 192 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 249 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 ASN ** G 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 270 ASN E 355 HIS E 392 GLN E 396 GLN C 141 HIS F 157 ASN F 204 GLN F 349 GLN F 355 HIS B 132 ASN B 341 GLN A 52 GLN A 159 GLN A 288 HIS A 332 ASN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS V 37 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23264 Z= 0.204 Angle : 0.625 10.960 31663 Z= 0.322 Chirality : 0.045 0.239 3490 Planarity : 0.005 0.048 4104 Dihedral : 5.952 58.972 3392 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 3.83 % Allowed : 16.29 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: -0.73 (0.15), residues: 2897 helix: -2.52 (0.54), residues: 66 sheet: 0.06 (0.15), residues: 1083 loop : -0.73 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 99 HIS 0.009 0.001 HIS H 52A PHE 0.030 0.002 PHE H 27 TYR 0.017 0.001 TYR G 122 ARG 0.005 0.000 ARG C 161 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 628 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Y 73 LEU cc_start: 0.6450 (tp) cc_final: 0.6202 (tp) REVERT: G 217 THR cc_start: 0.8531 (OUTLIER) cc_final: 0.8276 (p) REVERT: G 220 VAL cc_start: 0.8235 (p) cc_final: 0.7806 (t) REVERT: G 246 ASP cc_start: 0.6936 (m-30) cc_final: 0.6504 (m-30) REVERT: G 402 VAL cc_start: 0.3762 (OUTLIER) cc_final: 0.2517 (t) REVERT: E 15 TYR cc_start: 0.8444 (t80) cc_final: 0.7944 (t80) REVERT: E 94 CYS cc_start: 0.5794 (m) cc_final: 0.5402 (m) REVERT: E 304 ASN cc_start: 0.7081 (m110) cc_final: 0.6513 (m110) REVERT: E 311 ASP cc_start: 0.6866 (p0) cc_final: 0.6570 (p0) REVERT: E 315 ILE cc_start: 0.7698 (mm) cc_final: 0.7286 (mm) REVERT: E 319 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7706 (mmmt) REVERT: C 3 GLU cc_start: 0.7768 (tp30) cc_final: 0.7520 (tp30) REVERT: C 42 ASP cc_start: 0.6699 (p0) cc_final: 0.6322 (p0) REVERT: C 53 TYR cc_start: 0.8266 (m-80) cc_final: 0.8046 (m-80) REVERT: C 108 ASP cc_start: 0.6887 (m-30) cc_final: 0.6650 (m-30) REVERT: C 144 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6634 (mt-10) REVERT: C 313 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6826 (mt-10) REVERT: F 45 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7234 (mm-30) REVERT: F 75 ASP cc_start: 0.7957 (t70) cc_final: 0.7757 (t0) REVERT: F 99 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: F 260 GLU cc_start: 0.6495 (mt-10) cc_final: 0.6169 (mt-10) REVERT: F 309 SER cc_start: 0.7016 (t) cc_final: 0.6812 (p) REVERT: F 315 ILE cc_start: 0.7739 (mp) cc_final: 0.7483 (mm) REVERT: B 9 TYR cc_start: 0.8036 (m-80) cc_final: 0.7752 (m-80) REVERT: B 49 THR cc_start: 0.8150 (m) cc_final: 0.7944 (p) REVERT: B 148 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6977 (mm-30) REVERT: B 151 CYS cc_start: 0.5900 (p) cc_final: 0.5569 (p) REVERT: B 154 TYR cc_start: 0.8542 (m-80) cc_final: 0.8328 (m-80) REVERT: B 161 ARG cc_start: 0.7941 (tpp80) cc_final: 0.7266 (mpt180) REVERT: B 166 GLU cc_start: 0.7064 (mm-30) cc_final: 0.6796 (mm-30) REVERT: B 276 ILE cc_start: 0.8565 (mp) cc_final: 0.8289 (mt) REVERT: A 48 GLN cc_start: 0.8184 (tt0) cc_final: 0.7740 (tt0) REVERT: A 57 SER cc_start: 0.8565 (m) cc_final: 0.8048 (t) REVERT: A 124 SER cc_start: 0.8260 (t) cc_final: 0.7656 (p) REVERT: A 175 ASP cc_start: 0.7387 (t0) cc_final: 0.6987 (t0) REVERT: A 177 SER cc_start: 0.8585 (m) cc_final: 0.8017 (p) REVERT: A 275 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6702 (mtm) REVERT: A 276 ILE cc_start: 0.8869 (mm) cc_final: 0.8493 (mm) REVERT: A 288 HIS cc_start: 0.7475 (m-70) cc_final: 0.7078 (m90) REVERT: H 31 ASP cc_start: 0.7096 (m-30) cc_final: 0.6820 (m-30) REVERT: H 76 ASN cc_start: 0.8348 (t0) cc_final: 0.7997 (t0) REVERT: W 59 PHE cc_start: 0.7267 (m-80) cc_final: 0.6844 (m-80) REVERT: W 82 MET cc_start: 0.6231 (mmm) cc_final: 0.5718 (mmm) REVERT: V 2 MET cc_start: 0.3380 (tpt) cc_final: 0.3023 (tpt) outliers start: 94 outliers final: 61 residues processed: 667 average time/residue: 0.3278 time to fit residues: 338.8150 Evaluate side-chains 683 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 618 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 380 CYS Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 392 GLN Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 103 VAL Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 93 optimal weight: 3.9990 chunk 250 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 163 optimal weight: 0.0980 chunk 68 optimal weight: 0.9980 chunk 278 optimal weight: 0.0870 chunk 231 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN C 141 HIS F 10 GLN F 204 GLN F 355 HIS B 132 ASN B 288 HIS A 52 GLN A 132 ASN A 159 GLN A 216 GLN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23264 Z= 0.187 Angle : 0.604 10.983 31663 Z= 0.311 Chirality : 0.044 0.230 3490 Planarity : 0.005 0.047 4104 Dihedral : 5.629 56.364 3392 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 3.71 % Allowed : 17.47 % Favored : 78.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: -0.61 (0.15), residues: 2897 helix: -2.33 (0.57), residues: 66 sheet: 0.16 (0.15), residues: 1071 loop : -0.66 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP L 35 HIS 0.014 0.001 HIS E 394 PHE 0.028 0.002 PHE H 27 TYR 0.017 0.001 TYR B 238 ARG 0.008 0.000 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 637 time to evaluate : 2.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 112 ASP cc_start: 0.7853 (OUTLIER) cc_final: 0.7612 (m-30) REVERT: G 117 ASP cc_start: 0.7603 (t0) cc_final: 0.7269 (t70) REVERT: G 217 THR cc_start: 0.8433 (OUTLIER) cc_final: 0.8227 (p) REVERT: G 220 VAL cc_start: 0.8210 (p) cc_final: 0.7640 (t) REVERT: G 222 GLN cc_start: 0.7956 (mp10) cc_final: 0.7572 (mp10) REVERT: G 246 ASP cc_start: 0.6882 (m-30) cc_final: 0.6485 (m-30) REVERT: G 284 ASP cc_start: 0.7318 (OUTLIER) cc_final: 0.6837 (t0) REVERT: G 402 VAL cc_start: 0.3355 (OUTLIER) cc_final: 0.2059 (t) REVERT: E 5 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7374 (p) REVERT: E 15 TYR cc_start: 0.8425 (t80) cc_final: 0.7906 (t80) REVERT: E 94 CYS cc_start: 0.5808 (m) cc_final: 0.5337 (m) REVERT: E 238 SER cc_start: 0.7836 (OUTLIER) cc_final: 0.7552 (m) REVERT: E 304 ASN cc_start: 0.7033 (m110) cc_final: 0.6486 (m110) REVERT: E 311 ASP cc_start: 0.6880 (p0) cc_final: 0.6575 (p0) REVERT: E 319 LYS cc_start: 0.8117 (mmmt) cc_final: 0.7716 (mmmt) REVERT: E 327 LYS cc_start: 0.7537 (mmmm) cc_final: 0.7290 (mmmm) REVERT: C 3 GLU cc_start: 0.7773 (tp30) cc_final: 0.7533 (tp30) REVERT: C 42 ASP cc_start: 0.6684 (p0) cc_final: 0.6305 (p0) REVERT: C 53 TYR cc_start: 0.8200 (m-80) cc_final: 0.7999 (m-80) REVERT: C 81 GLN cc_start: 0.8330 (mm110) cc_final: 0.7631 (mt0) REVERT: C 108 ASP cc_start: 0.6857 (m-30) cc_final: 0.6621 (m-30) REVERT: C 120 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7576 (ttm110) REVERT: C 144 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6599 (mt-10) REVERT: C 313 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6805 (mt-10) REVERT: F 45 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7105 (mm-30) REVERT: F 75 ASP cc_start: 0.7881 (t70) cc_final: 0.7680 (t0) REVERT: F 315 ILE cc_start: 0.7735 (mp) cc_final: 0.7458 (mm) REVERT: B 9 TYR cc_start: 0.8017 (m-80) cc_final: 0.7783 (m-80) REVERT: B 112 MET cc_start: 0.8333 (ttt) cc_final: 0.8086 (ttp) REVERT: B 130 LYS cc_start: 0.8310 (mtmm) cc_final: 0.8087 (mtpp) REVERT: B 148 GLU cc_start: 0.7594 (mm-30) cc_final: 0.6993 (mm-30) REVERT: B 161 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7254 (mpt180) REVERT: B 166 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6782 (mm-30) REVERT: B 275 MET cc_start: 0.7199 (mtm) cc_final: 0.6989 (mtp) REVERT: A 21 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7278 (mtp85) REVERT: A 48 GLN cc_start: 0.8185 (tt0) cc_final: 0.7705 (tt0) REVERT: A 57 SER cc_start: 0.8549 (m) cc_final: 0.8063 (t) REVERT: A 124 SER cc_start: 0.8217 (t) cc_final: 0.7622 (p) REVERT: A 175 ASP cc_start: 0.7408 (t0) cc_final: 0.6954 (t0) REVERT: A 177 SER cc_start: 0.8619 (m) cc_final: 0.7998 (p) REVERT: A 263 ASP cc_start: 0.7738 (m-30) cc_final: 0.7432 (m-30) REVERT: A 276 ILE cc_start: 0.8884 (mm) cc_final: 0.8665 (mm) REVERT: A 330 TRP cc_start: 0.7795 (t60) cc_final: 0.7121 (t60) REVERT: H 31 ASP cc_start: 0.7116 (m-30) cc_final: 0.6837 (m-30) REVERT: H 76 ASN cc_start: 0.8363 (t0) cc_final: 0.8047 (t0) REVERT: W 59 PHE cc_start: 0.7295 (m-80) cc_final: 0.6891 (m-80) REVERT: W 82 MET cc_start: 0.6083 (mmm) cc_final: 0.5602 (mmm) REVERT: V 2 MET cc_start: 0.3231 (tpt) cc_final: 0.3014 (tpt) outliers start: 91 outliers final: 61 residues processed: 676 average time/residue: 0.3423 time to fit residues: 357.9952 Evaluate side-chains 694 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 626 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 380 CYS Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 112 ASP Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 394 HIS Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 268 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 155 optimal weight: 0.0670 chunk 277 optimal weight: 5.9990 chunk 173 optimal weight: 0.0980 chunk 169 optimal weight: 0.0170 chunk 128 optimal weight: 3.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 ASN ** G 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS F 10 GLN F 157 ASN F 204 GLN F 349 GLN B 132 ASN B 149 GLN B 288 HIS A 132 ASN A 159 GLN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23264 Z= 0.189 Angle : 0.597 10.348 31663 Z= 0.307 Chirality : 0.044 0.221 3490 Planarity : 0.005 0.047 4104 Dihedral : 5.426 54.326 3392 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.91 % Allowed : 18.00 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: -0.54 (0.15), residues: 2897 helix: -2.24 (0.59), residues: 66 sheet: 0.18 (0.15), residues: 1098 loop : -0.61 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 99 HIS 0.009 0.001 HIS C 141 PHE 0.035 0.002 PHE H 67 TYR 0.015 0.001 TYR C 238 ARG 0.007 0.000 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 627 time to evaluate : 2.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 112 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7611 (m-30) REVERT: G 117 ASP cc_start: 0.7585 (t0) cc_final: 0.7267 (t70) REVERT: G 217 THR cc_start: 0.8440 (OUTLIER) cc_final: 0.8214 (p) REVERT: G 220 VAL cc_start: 0.8206 (p) cc_final: 0.7778 (t) REVERT: G 233 TYR cc_start: 0.8411 (p90) cc_final: 0.8003 (p90) REVERT: G 246 ASP cc_start: 0.6922 (m-30) cc_final: 0.6492 (m-30) REVERT: G 284 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6825 (t0) REVERT: G 402 VAL cc_start: 0.3371 (OUTLIER) cc_final: 0.2066 (t) REVERT: E 5 THR cc_start: 0.7713 (OUTLIER) cc_final: 0.7410 (p) REVERT: E 94 CYS cc_start: 0.5733 (m) cc_final: 0.5258 (m) REVERT: E 238 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.7564 (m) REVERT: E 270 ASN cc_start: 0.8302 (m-40) cc_final: 0.7911 (m-40) REVERT: E 304 ASN cc_start: 0.7013 (m110) cc_final: 0.6486 (m110) REVERT: E 311 ASP cc_start: 0.6881 (p0) cc_final: 0.6594 (p0) REVERT: E 319 LYS cc_start: 0.8108 (mmmt) cc_final: 0.7693 (mmmt) REVERT: E 327 LYS cc_start: 0.7523 (mmmm) cc_final: 0.7289 (mmmm) REVERT: C 3 GLU cc_start: 0.7776 (tp30) cc_final: 0.7536 (tp30) REVERT: C 42 ASP cc_start: 0.6710 (p0) cc_final: 0.6340 (p0) REVERT: C 81 GLN cc_start: 0.8330 (mm110) cc_final: 0.7683 (mt0) REVERT: C 108 ASP cc_start: 0.6724 (m-30) cc_final: 0.6480 (m-30) REVERT: C 120 ARG cc_start: 0.7752 (ttm110) cc_final: 0.7548 (ttm110) REVERT: C 144 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6612 (mt-10) REVERT: C 313 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6791 (mt-10) REVERT: F 45 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7138 (mm-30) REVERT: F 75 ASP cc_start: 0.7898 (t70) cc_final: 0.7618 (t0) REVERT: F 315 ILE cc_start: 0.7830 (mp) cc_final: 0.7539 (mm) REVERT: F 402 VAL cc_start: 0.4649 (p) cc_final: 0.3300 (m) REVERT: B 9 TYR cc_start: 0.8011 (m-80) cc_final: 0.7766 (m-80) REVERT: B 148 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7075 (mm-30) REVERT: B 166 GLU cc_start: 0.7047 (mm-30) cc_final: 0.6756 (mm-30) REVERT: B 197 LEU cc_start: 0.8616 (tt) cc_final: 0.8297 (tp) REVERT: A 21 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7290 (mtp85) REVERT: A 48 GLN cc_start: 0.8154 (tt0) cc_final: 0.7712 (tt0) REVERT: A 57 SER cc_start: 0.8603 (m) cc_final: 0.8097 (t) REVERT: A 124 SER cc_start: 0.8188 (t) cc_final: 0.7609 (p) REVERT: A 175 ASP cc_start: 0.7467 (t0) cc_final: 0.6933 (t0) REVERT: A 177 SER cc_start: 0.8609 (m) cc_final: 0.7999 (p) REVERT: A 216 GLN cc_start: 0.7446 (tt0) cc_final: 0.6999 (tt0) REVERT: A 224 GLU cc_start: 0.7399 (tp30) cc_final: 0.7111 (mp0) REVERT: A 263 ASP cc_start: 0.7735 (m-30) cc_final: 0.7420 (m-30) REVERT: A 275 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6719 (mtm) REVERT: A 276 ILE cc_start: 0.8872 (mm) cc_final: 0.8661 (mm) REVERT: A 330 TRP cc_start: 0.7791 (t60) cc_final: 0.7132 (t60) REVERT: H 31 ASP cc_start: 0.7138 (m-30) cc_final: 0.6853 (m-30) REVERT: H 76 ASN cc_start: 0.8341 (t0) cc_final: 0.8045 (t0) REVERT: W 59 PHE cc_start: 0.7240 (m-80) cc_final: 0.6962 (m-80) REVERT: W 82 MET cc_start: 0.5961 (mmm) cc_final: 0.5573 (mmm) REVERT: V 2 MET cc_start: 0.3471 (tpt) cc_final: 0.3267 (tpt) REVERT: V 89 GLN cc_start: 0.7859 (tm-30) cc_final: 0.7647 (tm-30) outliers start: 96 outliers final: 66 residues processed: 669 average time/residue: 0.3341 time to fit residues: 346.1779 Evaluate side-chains 694 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 620 time to evaluate : 2.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 380 CYS Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain W residue 100 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 171 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 83 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 176 optimal weight: 0.5980 chunk 189 optimal weight: 0.0670 chunk 137 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 218 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 ASN ** G 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 140 HIS C 141 HIS F 10 GLN F 157 ASN B 132 ASN B 149 GLN B 152 GLN A 132 ASN A 159 GLN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23264 Z= 0.223 Angle : 0.607 11.131 31663 Z= 0.311 Chirality : 0.044 0.220 3490 Planarity : 0.005 0.046 4104 Dihedral : 5.421 54.444 3392 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.87 % Allowed : 18.44 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: -0.55 (0.15), residues: 2897 helix: -2.23 (0.59), residues: 66 sheet: 0.21 (0.16), residues: 1083 loop : -0.65 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 99 HIS 0.009 0.001 HIS C 141 PHE 0.030 0.002 PHE H 67 TYR 0.018 0.001 TYR E 15 ARG 0.007 0.000 ARG V 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 626 time to evaluate : 2.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 112 ASP cc_start: 0.7849 (OUTLIER) cc_final: 0.7624 (m-30) REVERT: G 117 ASP cc_start: 0.7600 (t0) cc_final: 0.7299 (t70) REVERT: G 217 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8242 (p) REVERT: G 220 VAL cc_start: 0.8209 (p) cc_final: 0.7806 (t) REVERT: G 233 TYR cc_start: 0.8423 (p90) cc_final: 0.8000 (p90) REVERT: G 238 SER cc_start: 0.8161 (p) cc_final: 0.7912 (p) REVERT: G 246 ASP cc_start: 0.6922 (m-30) cc_final: 0.6493 (m-30) REVERT: G 284 ASP cc_start: 0.7320 (OUTLIER) cc_final: 0.6731 (t0) REVERT: G 402 VAL cc_start: 0.3428 (OUTLIER) cc_final: 0.2108 (t) REVERT: E 5 THR cc_start: 0.7758 (OUTLIER) cc_final: 0.7467 (p) REVERT: E 114 CYS cc_start: 0.5491 (t) cc_final: 0.4953 (t) REVERT: E 135 ILE cc_start: 0.8254 (mp) cc_final: 0.7972 (mt) REVERT: E 238 SER cc_start: 0.7815 (OUTLIER) cc_final: 0.7590 (m) REVERT: E 304 ASN cc_start: 0.7034 (m110) cc_final: 0.6509 (m110) REVERT: E 311 ASP cc_start: 0.6887 (p0) cc_final: 0.6599 (p0) REVERT: E 319 LYS cc_start: 0.8111 (mmmt) cc_final: 0.7700 (mmmt) REVERT: C 3 GLU cc_start: 0.7785 (tp30) cc_final: 0.7541 (tp30) REVERT: C 42 ASP cc_start: 0.6738 (p0) cc_final: 0.6349 (p0) REVERT: C 53 TYR cc_start: 0.8220 (m-80) cc_final: 0.7964 (m-80) REVERT: C 81 GLN cc_start: 0.8342 (mm110) cc_final: 0.7712 (mt0) REVERT: C 108 ASP cc_start: 0.6723 (m-30) cc_final: 0.6477 (m-30) REVERT: C 144 GLU cc_start: 0.6968 (mt-10) cc_final: 0.6615 (mt-10) REVERT: C 313 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6790 (mt-10) REVERT: F 45 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7145 (mm-30) REVERT: F 75 ASP cc_start: 0.7931 (t70) cc_final: 0.7636 (t0) REVERT: F 304 ASN cc_start: 0.7644 (m-40) cc_final: 0.7426 (m110) REVERT: F 402 VAL cc_start: 0.4705 (p) cc_final: 0.3345 (m) REVERT: B 112 MET cc_start: 0.8374 (ttt) cc_final: 0.8118 (ttp) REVERT: B 130 LYS cc_start: 0.8310 (mtmm) cc_final: 0.7963 (mtpp) REVERT: B 148 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7074 (mm-30) REVERT: B 157 ASP cc_start: 0.7334 (t0) cc_final: 0.5860 (t0) REVERT: B 161 ARG cc_start: 0.7972 (tpp80) cc_final: 0.7145 (mpt180) REVERT: B 166 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6754 (mm-30) REVERT: B 197 LEU cc_start: 0.8595 (tt) cc_final: 0.8236 (tp) REVERT: A 21 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7282 (mtp85) REVERT: A 48 GLN cc_start: 0.8145 (tt0) cc_final: 0.7715 (tt0) REVERT: A 57 SER cc_start: 0.8594 (m) cc_final: 0.8107 (t) REVERT: A 124 SER cc_start: 0.8201 (t) cc_final: 0.7621 (p) REVERT: A 175 ASP cc_start: 0.7480 (t0) cc_final: 0.7020 (t0) REVERT: A 177 SER cc_start: 0.8623 (m) cc_final: 0.7989 (p) REVERT: A 216 GLN cc_start: 0.7456 (tt0) cc_final: 0.6990 (tt0) REVERT: A 275 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6725 (mtm) REVERT: A 276 ILE cc_start: 0.8901 (mm) cc_final: 0.8689 (mm) REVERT: A 287 LEU cc_start: 0.8180 (mp) cc_final: 0.7980 (mt) REVERT: A 316 VAL cc_start: 0.8492 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 330 TRP cc_start: 0.7803 (t60) cc_final: 0.7149 (t60) REVERT: H 31 ASP cc_start: 0.7133 (m-30) cc_final: 0.6850 (m-30) REVERT: H 76 ASN cc_start: 0.8346 (t0) cc_final: 0.8039 (t0) REVERT: W 59 PHE cc_start: 0.7215 (m-80) cc_final: 0.6939 (m-80) REVERT: W 82 MET cc_start: 0.5982 (mmm) cc_final: 0.5693 (mmm) REVERT: V 89 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7629 (tm-30) outliers start: 95 outliers final: 75 residues processed: 672 average time/residue: 0.3443 time to fit residues: 356.9433 Evaluate side-chains 705 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 621 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 171 THR Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 380 CYS Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 157 ASN Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 89 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 252 optimal weight: 7.9990 chunk 265 optimal weight: 1.9990 chunk 242 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 233 optimal weight: 2.9990 chunk 244 optimal weight: 10.0000 chunk 257 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS F 10 GLN F 204 GLN B 132 ASN B 149 GLN B 152 GLN A 132 ASN A 159 GLN A 288 HIS A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS V 37 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 23264 Z= 0.396 Angle : 0.675 11.737 31663 Z= 0.350 Chirality : 0.046 0.224 3490 Planarity : 0.005 0.050 4104 Dihedral : 5.806 59.960 3392 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.15 % Allowed : 18.49 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: -0.73 (0.15), residues: 2897 helix: -2.37 (0.57), residues: 66 sheet: 0.10 (0.15), residues: 1092 loop : -0.77 (0.15), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 35 HIS 0.011 0.001 HIS G 3 PHE 0.031 0.002 PHE H 67 TYR 0.023 0.002 TYR E 51 ARG 0.008 0.001 ARG B 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 633 time to evaluate : 2.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 67 PHE cc_start: 0.7162 (m-80) cc_final: 0.6826 (m-80) REVERT: Y 73 LEU cc_start: 0.6575 (tp) cc_final: 0.6200 (tp) REVERT: G 112 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7608 (m-30) REVERT: G 117 ASP cc_start: 0.7698 (t0) cc_final: 0.7414 (t70) REVERT: G 220 VAL cc_start: 0.8198 (p) cc_final: 0.7805 (t) REVERT: G 233 TYR cc_start: 0.8476 (p90) cc_final: 0.8022 (p90) REVERT: G 238 SER cc_start: 0.8213 (p) cc_final: 0.7869 (p) REVERT: G 241 GLU cc_start: 0.6780 (tt0) cc_final: 0.6267 (tt0) REVERT: G 246 ASP cc_start: 0.6929 (m-30) cc_final: 0.6509 (m-30) REVERT: G 264 ASN cc_start: 0.7863 (m-40) cc_final: 0.7613 (m-40) REVERT: G 284 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.6684 (t0) REVERT: G 402 VAL cc_start: 0.3762 (OUTLIER) cc_final: 0.2472 (t) REVERT: E 15 TYR cc_start: 0.8442 (t80) cc_final: 0.7986 (t80) REVERT: E 114 CYS cc_start: 0.5773 (t) cc_final: 0.5177 (t) REVERT: E 135 ILE cc_start: 0.8234 (mp) cc_final: 0.8007 (mt) REVERT: E 156 PHE cc_start: 0.6450 (m-80) cc_final: 0.6187 (m-10) REVERT: E 304 ASN cc_start: 0.7166 (m110) cc_final: 0.6636 (m110) REVERT: E 311 ASP cc_start: 0.6949 (p0) cc_final: 0.6678 (p0) REVERT: E 319 LYS cc_start: 0.8133 (mmmt) cc_final: 0.7698 (mmmt) REVERT: E 327 LYS cc_start: 0.7550 (mmmm) cc_final: 0.7321 (mmmm) REVERT: C 3 GLU cc_start: 0.7797 (tp30) cc_final: 0.7537 (tp30) REVERT: C 42 ASP cc_start: 0.6739 (p0) cc_final: 0.6390 (p0) REVERT: C 53 TYR cc_start: 0.8277 (m-80) cc_final: 0.7945 (m-80) REVERT: C 81 GLN cc_start: 0.8370 (mm110) cc_final: 0.7661 (mt0) REVERT: C 108 ASP cc_start: 0.6889 (m-30) cc_final: 0.6656 (m-30) REVERT: C 112 MET cc_start: 0.8234 (ttm) cc_final: 0.7765 (ttm) REVERT: C 144 GLU cc_start: 0.6984 (mt-10) cc_final: 0.6697 (mt-10) REVERT: C 313 GLU cc_start: 0.7093 (mt-10) cc_final: 0.6814 (mt-10) REVERT: F 45 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7247 (mm-30) REVERT: F 75 ASP cc_start: 0.7989 (t70) cc_final: 0.7662 (t0) REVERT: F 143 VAL cc_start: 0.7550 (OUTLIER) cc_final: 0.7333 (t) REVERT: F 186 ASN cc_start: 0.8505 (m-40) cc_final: 0.8199 (m-40) REVERT: F 260 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6077 (mt-10) REVERT: F 304 ASN cc_start: 0.7787 (m-40) cc_final: 0.7553 (m110) REVERT: F 402 VAL cc_start: 0.4292 (p) cc_final: 0.2954 (m) REVERT: B 69 ASP cc_start: 0.7301 (t70) cc_final: 0.7006 (t70) REVERT: B 130 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7994 (mtpp) REVERT: B 148 GLU cc_start: 0.7615 (mm-30) cc_final: 0.7073 (mm-30) REVERT: B 166 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6751 (mm-30) REVERT: B 238 TYR cc_start: 0.7560 (t80) cc_final: 0.7333 (t80) REVERT: A 21 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7324 (mtp85) REVERT: A 48 GLN cc_start: 0.8200 (tt0) cc_final: 0.7776 (tt0) REVERT: A 57 SER cc_start: 0.8559 (m) cc_final: 0.8072 (t) REVERT: A 124 SER cc_start: 0.8251 (t) cc_final: 0.7677 (p) REVERT: A 275 MET cc_start: 0.7362 (OUTLIER) cc_final: 0.6730 (mtm) REVERT: A 276 ILE cc_start: 0.8877 (mm) cc_final: 0.8654 (mm) REVERT: A 316 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8310 (p) REVERT: H 31 ASP cc_start: 0.7043 (m-30) cc_final: 0.6762 (m-30) REVERT: H 76 ASN cc_start: 0.8389 (t0) cc_final: 0.8009 (t0) REVERT: H 100 TYR cc_start: 0.8120 (t80) cc_final: 0.7670 (t80) REVERT: W 59 PHE cc_start: 0.7239 (m-80) cc_final: 0.6861 (m-80) REVERT: W 82 MET cc_start: 0.5946 (mmm) cc_final: 0.5653 (mtp) REVERT: V 89 GLN cc_start: 0.7948 (tm-30) cc_final: 0.7616 (tm-30) outliers start: 102 outliers final: 84 residues processed: 675 average time/residue: 0.3565 time to fit residues: 374.9503 Evaluate side-chains 709 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 618 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 371 THR Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 380 CYS Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 29 ILE Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 303 LEU Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 286 LYS Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 204 GLN Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain F residue 269 GLU Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain F residue 367 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain V residue 9 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 169 optimal weight: 1.9990 chunk 273 optimal weight: 0.0060 chunk 166 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 190 optimal weight: 0.0020 chunk 286 optimal weight: 4.9990 chunk 264 optimal weight: 5.9990 chunk 228 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 overall best weight: 0.7806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 157 ASN ** G 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS F 10 GLN F 157 ASN F 204 GLN B 132 ASN B 149 GLN B 152 GLN A 132 ASN A 216 GLN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23264 Z= 0.220 Angle : 0.630 12.025 31663 Z= 0.323 Chirality : 0.045 0.216 3490 Planarity : 0.005 0.047 4104 Dihedral : 5.565 57.648 3392 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.59 % Favored : 95.37 % Rotamer: Outliers : 3.46 % Allowed : 19.79 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.15), residues: 2897 helix: -2.28 (0.59), residues: 66 sheet: 0.17 (0.16), residues: 1083 loop : -0.69 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP L 35 HIS 0.009 0.001 HIS C 141 PHE 0.028 0.002 PHE H 67 TYR 0.019 0.001 TYR B 9 ARG 0.009 0.000 ARG V 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5794 Ramachandran restraints generated. 2897 Oldfield, 0 Emsley, 2897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 627 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 67 PHE cc_start: 0.7038 (m-80) cc_final: 0.6698 (m-80) REVERT: Y 73 LEU cc_start: 0.6483 (tp) cc_final: 0.6129 (tp) REVERT: G 112 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: G 217 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8320 (p) REVERT: G 220 VAL cc_start: 0.8186 (p) cc_final: 0.7783 (t) REVERT: G 233 TYR cc_start: 0.8452 (p90) cc_final: 0.8015 (p90) REVERT: G 238 SER cc_start: 0.8128 (p) cc_final: 0.7778 (p) REVERT: G 241 GLU cc_start: 0.6747 (tt0) cc_final: 0.6420 (tt0) REVERT: G 246 ASP cc_start: 0.6910 (m-30) cc_final: 0.6484 (m-30) REVERT: G 284 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6464 (t0) REVERT: G 402 VAL cc_start: 0.3460 (OUTLIER) cc_final: 0.2155 (t) REVERT: E 5 THR cc_start: 0.7858 (OUTLIER) cc_final: 0.7632 (p) REVERT: E 15 TYR cc_start: 0.8448 (t80) cc_final: 0.7991 (t80) REVERT: E 114 CYS cc_start: 0.5698 (t) cc_final: 0.5112 (t) REVERT: E 135 ILE cc_start: 0.8177 (mp) cc_final: 0.7932 (mt) REVERT: E 304 ASN cc_start: 0.7088 (m110) cc_final: 0.6566 (m110) REVERT: E 311 ASP cc_start: 0.6888 (p0) cc_final: 0.6606 (p0) REVERT: E 319 LYS cc_start: 0.8084 (mmmt) cc_final: 0.7658 (mmmt) REVERT: C 3 GLU cc_start: 0.7778 (tp30) cc_final: 0.7550 (tp30) REVERT: C 42 ASP cc_start: 0.6760 (p0) cc_final: 0.6386 (p0) REVERT: C 81 GLN cc_start: 0.8350 (mm110) cc_final: 0.7710 (mt0) REVERT: C 108 ASP cc_start: 0.6847 (m-30) cc_final: 0.6614 (m-30) REVERT: C 144 GLU cc_start: 0.6990 (mt-10) cc_final: 0.6690 (mt-10) REVERT: C 313 GLU cc_start: 0.7085 (mt-10) cc_final: 0.6809 (mt-10) REVERT: F 45 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7070 (mm-30) REVERT: F 75 ASP cc_start: 0.7999 (t70) cc_final: 0.7665 (t0) REVERT: F 143 VAL cc_start: 0.7471 (OUTLIER) cc_final: 0.7244 (t) REVERT: F 260 GLU cc_start: 0.6431 (mt-10) cc_final: 0.6012 (mt-10) REVERT: F 304 ASN cc_start: 0.7695 (m-40) cc_final: 0.7491 (m110) REVERT: F 402 VAL cc_start: 0.4069 (p) cc_final: 0.2730 (m) REVERT: B 112 MET cc_start: 0.8347 (ttt) cc_final: 0.8095 (ttp) REVERT: B 148 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7047 (mm-30) REVERT: B 166 GLU cc_start: 0.7029 (mm-30) cc_final: 0.6760 (mm-30) REVERT: A 21 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7257 (mtp85) REVERT: A 48 GLN cc_start: 0.8141 (tt0) cc_final: 0.7709 (tt0) REVERT: A 57 SER cc_start: 0.8640 (m) cc_final: 0.8101 (t) REVERT: A 124 SER cc_start: 0.8208 (t) cc_final: 0.7636 (p) REVERT: A 177 SER cc_start: 0.8581 (m) cc_final: 0.8079 (p) REVERT: A 224 GLU cc_start: 0.7453 (tp30) cc_final: 0.7144 (mp0) REVERT: A 263 ASP cc_start: 0.7703 (m-30) cc_final: 0.7464 (m-30) REVERT: A 275 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.6679 (mtm) REVERT: H 31 ASP cc_start: 0.7123 (m-30) cc_final: 0.6842 (m-30) REVERT: H 76 ASN cc_start: 0.8329 (t0) cc_final: 0.7975 (t0) REVERT: W 59 PHE cc_start: 0.7191 (m-80) cc_final: 0.6939 (m-80) REVERT: W 82 MET cc_start: 0.5851 (mmm) cc_final: 0.5550 (mtp) REVERT: V 54 ARG cc_start: 0.7459 (mtt-85) cc_final: 0.7231 (mtt180) REVERT: V 89 GLN cc_start: 0.7867 (tm-30) cc_final: 0.7594 (tm-30) outliers start: 85 outliers final: 69 residues processed: 662 average time/residue: 0.3422 time to fit residues: 349.4884 Evaluate side-chains 698 residues out of total 2456 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 621 time to evaluate : 2.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain X residue 77 THR Chi-restraints excluded: chain X residue 89 VAL Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 112 ASP Chi-restraints excluded: chain G residue 142 ILE Chi-restraints excluded: chain G residue 162 THR Chi-restraints excluded: chain G residue 204 GLN Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 234 THR Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 375 THR Chi-restraints excluded: chain G residue 380 CYS Chi-restraints excluded: chain G residue 385 ASP Chi-restraints excluded: chain G residue 389 THR Chi-restraints excluded: chain G residue 397 THR Chi-restraints excluded: chain G residue 402 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 42 VAL Chi-restraints excluded: chain E residue 55 MET Chi-restraints excluded: chain E residue 79 LYS Chi-restraints excluded: chain E residue 80 VAL Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 159 VAL Chi-restraints excluded: chain E residue 171 THR Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain C residue 12 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 308 HIS Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 143 VAL Chi-restraints excluded: chain F residue 207 THR Chi-restraints excluded: chain F residue 288 THR Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 347 THR Chi-restraints excluded: chain F residue 353 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 76 GLU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 209 GLU Chi-restraints excluded: chain B residue 222 LYS Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 341 GLN Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 12 THR Chi-restraints excluded: chain A residue 21 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain A residue 254 LYS Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 MET Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 89 VAL Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 181 optimal weight: 0.9990 chunk 243 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 210 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 228 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 392 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 10 GLN ** F 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN B 132 ASN B 149 GLN B 152 GLN A 132 ASN A 332 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 100DHIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.124989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109916 restraints weight = 37301.967| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.16 r_work: 0.3319 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23264 Z= 0.253 Angle : 0.632 12.271 31663 Z= 0.325 Chirality : 0.045 0.217 3490 Planarity : 0.005 0.046 4104 Dihedral : 5.549 57.457 3392 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.90 % Favored : 95.06 % Rotamer: Outliers : 3.50 % Allowed : 20.07 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.62 % 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: -0.60 (0.15), residues: 2897 helix: -2.25 (0.59), residues: 66 sheet: 0.17 (0.16), residues: 1083 loop : -0.68 (0.15), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP X 47 HIS 0.010 0.001 HIS C 141 PHE 0.029 0.002 PHE H 27 TYR 0.018 0.001 TYR B 68 ARG 0.008 0.000 ARG B 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6552.40 seconds wall clock time: 118 minutes 35.05 seconds (7115.05 seconds total)