Starting phenix.real_space_refine on Thu Feb 22 15:53:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttn_26120/02_2024/7ttn_26120_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttn_26120/02_2024/7ttn_26120.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/7ttn_26120/02_2024/7ttn_26120.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttn_26120/02_2024/7ttn_26120.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttn_26120/02_2024/7ttn_26120_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ttn_26120/02_2024/7ttn_26120_updated.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= 0.000 sd= 1.000 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: 8 Type Number sf(0) Gaussians Al 8 5.89 5 P 16 5.49 5 Mg 8 5.21 5 S 209 5.16 5 C 21598 2.51 5 N 6000 2.21 5 O 6700 1.98 5 F 24 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 111": "OE1" <-> "OE2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A PHE 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "B GLU 17": "OE1" <-> "OE2" Residue "B GLU 61": "OE1" <-> "OE2" Residue "B ASP 68": "OD1" <-> "OD2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B GLU 113": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B ASP 200": "OD1" <-> "OD2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B ASP 320": "OD1" <-> "OD2" Residue "B ASP 357": "OD1" <-> "OD2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B ASP 387": "OD1" <-> "OD2" Residue "B GLU 443": "OE1" <-> "OE2" Residue "B ASP 491": "OD1" <-> "OD2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "C ASP 46": "OD1" <-> "OD2" Residue "C ASP 61": "OD1" <-> "OD2" Residue "C ASP 87": "OD1" <-> "OD2" Residue "C GLU 103": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C ASP 188": "OD1" <-> "OD2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C ASP 340": "OD1" <-> "OD2" Residue "C GLU 349": "OE1" <-> "OE2" Residue "C PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 379": "OE1" <-> "OE2" Residue "C GLU 383": "OE1" <-> "OE2" Residue "C TYR 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 492": "OE1" <-> "OE2" Residue "C GLU 499": "OE1" <-> "OE2" Residue "C PHE 501": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 73": "OD1" <-> "OD2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D ASP 158": "OD1" <-> "OD2" Residue "D GLU 187": "OE1" <-> "OE2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "D ASP 233": "OD1" <-> "OD2" Residue "D GLU 272": "OE1" <-> "OE2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 369": "OD1" <-> "OD2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 508": "OE1" <-> "OE2" Residue "D ASP 532": "OD1" <-> "OD2" Residue "E ASP 66": "OD1" <-> "OD2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ASP 158": "OD1" <-> "OD2" Residue "E GLU 197": "OE1" <-> "OE2" Residue "E GLU 271": "OE1" <-> "OE2" Residue "E TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 369": "OE1" <-> "OE2" Residue "E ASP 403": "OD1" <-> "OD2" Residue "E TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 495": "OE1" <-> "OE2" Residue "F ASP 73": "OD1" <-> "OD2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F ASP 159": "OD1" <-> "OD2" Residue "F ASP 219": "OD1" <-> "OD2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F ASP 307": "OD1" <-> "OD2" Residue "F ASP 349": "OD1" <-> "OD2" Residue "F PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 363": "OE1" <-> "OE2" Residue "F GLU 402": "OE1" <-> "OE2" Residue "F TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 506": "OE1" <-> "OE2" Residue "G GLU 99": "OE1" <-> "OE2" Residue "G TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 146": "OD1" <-> "OD2" Residue "G TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 273": "OE1" <-> "OE2" Residue "G ASP 293": "OD1" <-> "OD2" Residue "G ASP 294": "OD1" <-> "OD2" Residue "G PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 519": "OE1" <-> "OE2" Residue "H ASP 52": "OD1" <-> "OD2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 104": "OE1" <-> "OE2" Residue "H ASP 150": "OD1" <-> "OD2" Residue "H TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 262": "OE1" <-> "OE2" Residue "H TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 393": "OD1" <-> "OD2" Residue "H GLU 497": "OE1" <-> "OE2" Residue "H GLU 511": "OE1" <-> "OE2" Residue "I ASP 90": "OD1" <-> "OD2" Residue "I GLU 101": "OE1" <-> "OE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "I GLU 142": "OE1" <-> "OE2" Residue "I PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 192": "OE1" <-> "OE2" Residue "I GLU 201": "OE1" <-> "OE2" Residue "I TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 240": "OE1" <-> "OE2" Residue "I TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 276": "OE1" <-> "OE2" Residue "I PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 461": "OE1" <-> "OE2" Residue "I ASP 496": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34563 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 2119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2119 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 9, 'TRANS': 259} Chain breaks: 3 Chain: "B" Number of atoms: 4029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 529, 4029 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 15, 'TRANS': 513} Chain: "C" Number of atoms: 4003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4003 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 15, 'TRANS': 505} Chain breaks: 1 Chain: "D" Number of atoms: 4072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4072 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 18, 'TRANS': 509} Chain: "E" Number of atoms: 3974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 3974 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 11, 'TRANS': 516} Chain: "F" Number of atoms: 3924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3924 Classifications: {'peptide': 520} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "G" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4063 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 14, 'TRANS': 520} Chain: "H" Number of atoms: 4064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4064 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} Chain: "I" Number of atoms: 4051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4051 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 14, 'TRANS': 513} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 18.08, per 1000 atoms: 0.52 Number of scatterers: 34563 At special positions: 0 Unit cell: (180.4, 183.7, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 209 16.00 P 16 15.00 Al 8 13.00 Mg 8 11.99 F 24 9.00 O 6700 8.00 N 6000 7.00 C 21598 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "HETATM34418 O3A ADP E 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM34546 O3A ADP I 602 .*. O " rejected from bonding due to valence issues. Atom "HETATM34326 O3A ADP B 603 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.53 Conformation dependent library (CDL) restraints added in 6.3 seconds 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8340 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 169 helices and 51 sheets defined 46.7% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.03 Creating SS restraints... Processing helix chain 'A' and resid 10 through 25 removed outlier: 3.523A pdb=" N LYS A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLU A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N VAL A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 109 through 126 removed outlier: 3.535A pdb=" N VAL A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ASP A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP A 118 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS A 122 " --> pdb=" O ASP A 118 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 158 removed outlier: 3.795A pdb=" N MET A 147 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 157 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N GLU A 158 " --> pdb=" O LYS A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 189 removed outlier: 3.860A pdb=" N LEU A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER A 188 " --> pdb=" O ASN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 390 removed outlier: 3.572A pdb=" N ILE A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 382 " --> pdb=" O PHE A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 401 removed outlier: 4.640A pdb=" N GLU A 401 " --> pdb=" O TRP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 Processing helix chain 'B' and resid 11 through 13 No H-bonds generated for 'chain 'B' and resid 11 through 13' Processing helix chain 'B' and resid 29 through 43 removed outlier: 3.722A pdb=" N GLN B 34 " --> pdb=" O TYR B 30 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 40 " --> pdb=" O CYS B 36 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 41 " --> pdb=" O LYS B 37 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 81 through 96 removed outlier: 3.676A pdb=" N MET B 85 " --> pdb=" O PRO B 81 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN B 95 " --> pdb=" O HIS B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 120 removed outlier: 3.834A pdb=" N LEU B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 112 " --> pdb=" O ALA B 108 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 113 " --> pdb=" O GLY B 109 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU B 116 " --> pdb=" O LEU B 112 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 120 " --> pdb=" O GLU B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 146 removed outlier: 3.501A pdb=" N GLU B 141 " --> pdb=" O ARG B 137 " (cutoff:3.500A) Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 165 through 169 Processing helix chain 'B' and resid 176 through 187 removed outlier: 3.559A pdb=" N ALA B 180 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS B 181 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 214 No H-bonds generated for 'chain 'B' and resid 212 through 214' Processing helix chain 'B' and resid 262 through 286 removed outlier: 3.669A pdb=" N ASN B 267 " --> pdb=" O GLU B 263 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS B 270 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 307 removed outlier: 3.658A pdb=" N TYR B 304 " --> pdb=" O MET B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 328 removed outlier: 3.538A pdb=" N LYS B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 404 removed outlier: 3.617A pdb=" N ASP B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 429 removed outlier: 3.790A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 422 " --> pdb=" O GLU B 418 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR B 429 " --> pdb=" O SER B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 456 removed outlier: 3.969A pdb=" N PHE B 445 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLU B 446 " --> pdb=" O ALA B 442 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ALA B 447 " --> pdb=" O GLU B 443 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Proline residue: B 449 - end of helix Processing helix chain 'B' and resid 460 through 473 removed outlier: 3.726A pdb=" N ALA B 469 " --> pdb=" O SER B 465 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU B 473 " --> pdb=" O ALA B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 495 No H-bonds generated for 'chain 'B' and resid 492 through 495' Processing helix chain 'B' and resid 501 through 520 removed outlier: 3.511A pdb=" N TRP B 506 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 507 " --> pdb=" O GLY B 503 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS B 509 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL B 518 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG B 520 " --> pdb=" O VAL B 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 26 removed outlier: 3.635A pdb=" N ASN C 25 " --> pdb=" O GLN C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'C' and resid 62 through 67 Processing helix chain 'C' and resid 76 through 89 removed outlier: 3.702A pdb=" N VAL C 80 " --> pdb=" O LYS C 77 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE C 82 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 83 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASP C 87 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU C 89 " --> pdb=" O GLN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 106 removed outlier: 3.519A pdb=" N LEU C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU C 105 " --> pdb=" O ALA C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 118 through 138 removed outlier: 3.546A pdb=" N ASN C 134 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS C 135 " --> pdb=" O LEU C 131 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS C 137 " --> pdb=" O VAL C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 162 removed outlier: 4.171A pdb=" N LEU C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 184 removed outlier: 3.631A pdb=" N LYS C 177 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET C 178 " --> pdb=" O PHE C 174 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASP C 181 " --> pdb=" O LYS C 177 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 207 No H-bonds generated for 'chain 'C' and resid 205 through 207' Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 260 through 284 removed outlier: 3.563A pdb=" N ALA C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N TRP C 271 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER C 284 " --> pdb=" O LYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 316 through 326 removed outlier: 3.770A pdb=" N ARG C 321 " --> pdb=" O GLU C 317 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET C 324 " --> pdb=" O LYS C 320 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 325 " --> pdb=" O ARG C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 379 through 401 removed outlier: 3.610A pdb=" N ASP C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET C 394 " --> pdb=" O HIS C 390 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS C 401 " --> pdb=" O ARG C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 424 removed outlier: 3.709A pdb=" N GLU C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 416 " --> pdb=" O ILE C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 439 removed outlier: 3.702A pdb=" N GLN C 432 " --> pdb=" O GLY C 429 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 433 " --> pdb=" O LYS C 430 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 435 " --> pdb=" O GLN C 432 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLY C 436 " --> pdb=" O LEU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 453 removed outlier: 4.144A pdb=" N ILE C 445 " --> pdb=" O LEU C 442 " (cutoff:3.500A) Proline residue: C 446 - end of helix removed outlier: 3.940A pdb=" N ASN C 452 " --> pdb=" O LEU C 449 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA C 453 " --> pdb=" O CYS C 450 " (cutoff:3.500A) Processing helix chain 'C' and resid 457 through 470 removed outlier: 3.827A pdb=" N LEU C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 470 " --> pdb=" O ALA C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 525 removed outlier: 3.608A pdb=" N ASN C 511 " --> pdb=" O MET C 507 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA C 512 " --> pdb=" O VAL C 508 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER C 525 " --> pdb=" O CYS C 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 30 through 47 removed outlier: 3.854A pdb=" N LEU D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE D 38 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA D 45 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 removed outlier: 3.517A pdb=" N LEU D 78 " --> pdb=" O GLY D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 99 removed outlier: 3.721A pdb=" N GLN D 98 " --> pdb=" O LEU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 126 removed outlier: 3.514A pdb=" N GLU D 119 " --> pdb=" O ALA D 115 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ALA D 120 " --> pdb=" O LEU D 116 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN D 122 " --> pdb=" O GLU D 118 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LEU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 148 removed outlier: 3.960A pdb=" N GLU D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 174 removed outlier: 3.895A pdb=" N THR D 171 " --> pdb=" O GLN D 167 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N THR D 172 " --> pdb=" O THR D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 removed outlier: 3.952A pdb=" N ALA D 189 " --> pdb=" O MET D 185 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL D 190 " --> pdb=" O ALA D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'D' and resid 219 through 221 No H-bonds generated for 'chain 'D' and resid 219 through 221' Processing helix chain 'D' and resid 271 through 294 removed outlier: 3.542A pdb=" N GLU D 286 " --> pdb=" O LYS D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 316 removed outlier: 4.106A pdb=" N HIS D 312 " --> pdb=" O ASP D 308 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU D 314 " --> pdb=" O ALA D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 337 removed outlier: 3.856A pdb=" N GLU D 331 " --> pdb=" O GLY D 327 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 332 " --> pdb=" O PRO D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 392 through 414 removed outlier: 3.604A pdb=" N GLU D 396 " --> pdb=" O LYS D 392 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG D 414 " --> pdb=" O ARG D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 439 removed outlier: 3.855A pdb=" N ASP D 438 " --> pdb=" O SER D 434 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LYS D 439 " --> pdb=" O GLN D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 466 removed outlier: 3.983A pdb=" N GLU D 456 " --> pdb=" O ALA D 452 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL D 457 " --> pdb=" O ASP D 453 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ILE D 458 " --> pdb=" O ALA D 454 " (cutoff:3.500A) Proline residue: D 459 - end of helix removed outlier: 3.635A pdb=" N GLU D 464 " --> pdb=" O MET D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 483 removed outlier: 3.508A pdb=" N THR D 475 " --> pdb=" O ILE D 471 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLU D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 504 No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'D' and resid 510 through 529 removed outlier: 3.509A pdb=" N GLN D 516 " --> pdb=" O GLY D 512 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE D 517 " --> pdb=" O LYS D 513 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA D 520 " --> pdb=" O GLN D 516 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET D 523 " --> pdb=" O LEU D 519 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL D 524 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET D 526 " --> pdb=" O GLN D 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 42 removed outlier: 4.150A pdb=" N LEU E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA E 32 " --> pdb=" O SER E 28 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE E 35 " --> pdb=" O GLY E 31 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL E 39 " --> pdb=" O ILE E 35 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N SER E 41 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 69 through 73 Processing helix chain 'E' and resid 79 through 94 removed outlier: 3.779A pdb=" N VAL E 83 " --> pdb=" O ALA E 80 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 84 " --> pdb=" O ALA E 81 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL E 85 " --> pdb=" O LYS E 82 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET E 87 " --> pdb=" O LEU E 84 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER E 88 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL E 90 " --> pdb=" O MET E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 117 removed outlier: 3.772A pdb=" N LEU E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER E 115 " --> pdb=" O ARG E 111 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE E 117 " --> pdb=" O ALA E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 144 removed outlier: 3.874A pdb=" N GLU E 132 " --> pdb=" O ALA E 128 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA E 133 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 166 removed outlier: 3.910A pdb=" N GLN E 157 " --> pdb=" O VAL E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 176 through 190 removed outlier: 4.467A pdb=" N LYS E 181 " --> pdb=" O ASP E 177 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 182 " --> pdb=" O HIS E 178 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA E 186 " --> pdb=" O LEU E 182 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL E 187 " --> pdb=" O ALA E 183 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU E 188 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LEU E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 198 No H-bonds generated for 'chain 'E' and resid 196 through 198' Processing helix chain 'E' and resid 209 through 211 No H-bonds generated for 'chain 'E' and resid 209 through 211' Processing helix chain 'E' and resid 261 through 285 removed outlier: 3.521A pdb=" N ALA E 265 " --> pdb=" O THR E 261 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS E 276 " --> pdb=" O LYS E 272 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU E 277 " --> pdb=" O GLU E 273 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS E 285 " --> pdb=" O ARG E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 306 removed outlier: 3.720A pdb=" N GLN E 302 " --> pdb=" O ASN E 298 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU E 303 " --> pdb=" O TYR E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 326 removed outlier: 4.000A pdb=" N ARG E 322 " --> pdb=" O ALA E 318 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU E 323 " --> pdb=" O GLY E 319 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU E 325 " --> pdb=" O GLU E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 402 removed outlier: 3.619A pdb=" N ASP E 392 " --> pdb=" O ARG E 388 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA E 393 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN E 399 " --> pdb=" O CYS E 395 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR E 400 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL E 401 " --> pdb=" O LEU E 397 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS E 402 " --> pdb=" O ALA E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 425 removed outlier: 3.582A pdb=" N ALA E 420 " --> pdb=" O LEU E 416 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 453 removed outlier: 3.656A pdb=" N MET E 436 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU E 443 " --> pdb=" O ALA E 440 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG E 444 " --> pdb=" O LYS E 441 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET E 445 " --> pdb=" O ALA E 442 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU E 446 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Proline residue: E 447 - end of helix removed outlier: 3.526A pdb=" N ILE E 450 " --> pdb=" O PRO E 447 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN E 453 " --> pdb=" O ILE E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 469 removed outlier: 4.002A pdb=" N ALA E 463 " --> pdb=" O ALA E 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 488 through 491 No H-bonds generated for 'chain 'E' and resid 488 through 491' Processing helix chain 'E' and resid 497 through 515 removed outlier: 3.646A pdb=" N LEU E 504 " --> pdb=" O LYS E 500 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA E 511 " --> pdb=" O ALA E 507 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 47 removed outlier: 3.518A pdb=" N SER F 39 " --> pdb=" O PHE F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 74 through 80 removed outlier: 3.592A pdb=" N LEU F 78 " --> pdb=" O GLY F 74 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 101 removed outlier: 3.552A pdb=" N MET F 90 " --> pdb=" O PRO F 86 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU F 93 " --> pdb=" O ARG F 89 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA F 97 " --> pdb=" O GLU F 93 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 125 removed outlier: 3.919A pdb=" N VAL F 110 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASP F 118 " --> pdb=" O GLY F 114 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS F 120 " --> pdb=" O LEU F 116 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS F 122 " --> pdb=" O ASP F 118 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU F 123 " --> pdb=" O SER F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 149 removed outlier: 3.856A pdb=" N GLU F 146 " --> pdb=" O GLU F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 169 Processing helix chain 'F' and resid 177 through 192 removed outlier: 3.832A pdb=" N SER F 180 " --> pdb=" O SER F 177 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER F 181 " --> pdb=" O GLN F 178 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU F 182 " --> pdb=" O TYR F 179 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU F 183 " --> pdb=" O SER F 180 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N SER F 184 " --> pdb=" O SER F 181 " (cutoff:3.500A) Proline residue: F 185 - end of helix removed outlier: 3.599A pdb=" N VAL F 188 " --> pdb=" O PRO F 185 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN F 189 " --> pdb=" O MET F 186 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET F 192 " --> pdb=" O ASN F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 207 No H-bonds generated for 'chain 'F' and resid 205 through 207' Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 269 through 293 removed outlier: 4.366A pdb=" N ASP F 273 " --> pdb=" O TYR F 269 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG F 274 " --> pdb=" O ALA F 270 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU F 276 " --> pdb=" O MET F 272 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR F 293 " --> pdb=" O GLN F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 320 removed outlier: 3.724A pdb=" N LYS F 319 " --> pdb=" O HIS F 315 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 339 Processing helix chain 'F' and resid 348 through 350 No H-bonds generated for 'chain 'F' and resid 348 through 350' Processing helix chain 'F' and resid 395 through 417 removed outlier: 3.563A pdb=" N GLU F 399 " --> pdb=" O LYS F 395 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE F 412 " --> pdb=" O ALA F 408 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL F 416 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS F 417 " --> pdb=" O ARG F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 442 removed outlier: 3.554A pdb=" N GLU F 431 " --> pdb=" O ALA F 427 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N THR F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU F 438 " --> pdb=" O LEU F 434 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG F 441 " --> pdb=" O THR F 437 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N THR F 442 " --> pdb=" O GLU F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 447 through 468 removed outlier: 3.790A pdb=" N ARG F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N MET F 458 " --> pdb=" O PHE F 454 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU F 459 " --> pdb=" O ALA F 455 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N VAL F 460 " --> pdb=" O ASP F 456 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ILE F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) Proline residue: F 462 - end of helix removed outlier: 3.700A pdb=" N ALA F 466 " --> pdb=" O PRO F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 473 through 484 Processing helix chain 'F' and resid 503 through 506 Processing helix chain 'F' and resid 512 through 531 removed outlier: 3.804A pdb=" N LEU F 519 " --> pdb=" O SER F 515 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU F 521 " --> pdb=" O SER F 517 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA F 522 " --> pdb=" O ALA F 518 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS F 531 " --> pdb=" O ARG F 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 18 No H-bonds generated for 'chain 'G' and resid 15 through 18' Processing helix chain 'G' and resid 23 through 34 removed outlier: 3.743A pdb=" N ILE G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL G 32 " --> pdb=" O ILE G 28 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER G 34 " --> pdb=" O ASN G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 64 removed outlier: 3.623A pdb=" N LYS G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 70 through 85 removed outlier: 3.840A pdb=" N VAL G 74 " --> pdb=" O PRO G 70 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LEU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS G 84 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 109 removed outlier: 3.640A pdb=" N ILE G 96 " --> pdb=" O SER G 92 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU G 101 " --> pdb=" O ALA G 97 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU G 106 " --> pdb=" O LYS G 102 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU G 107 " --> pdb=" O ASN G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 114 through 134 removed outlier: 3.509A pdb=" N ARG G 130 " --> pdb=" O LYS G 126 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE G 132 " --> pdb=" O ALA G 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 156 removed outlier: 3.793A pdb=" N SER G 155 " --> pdb=" O ALA G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 179 removed outlier: 4.486A pdb=" N ASP G 166 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ALA G 169 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN G 170 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL G 173 " --> pdb=" O ASN G 170 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU G 177 " --> pdb=" O ASP G 174 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA G 178 " --> pdb=" O ALA G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 207 No H-bonds generated for 'chain 'G' and resid 205 through 207' Processing helix chain 'G' and resid 257 through 259 No H-bonds generated for 'chain 'G' and resid 257 through 259' Processing helix chain 'G' and resid 261 through 266 Processing helix chain 'G' and resid 270 through 281 removed outlier: 4.447A pdb=" N THR G 281 " --> pdb=" O LYS G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 302 No H-bonds generated for 'chain 'G' and resid 299 through 302' Processing helix chain 'G' and resid 313 through 323 removed outlier: 3.816A pdb=" N ARG G 318 " --> pdb=" O ARG G 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 404 removed outlier: 3.515A pdb=" N GLU G 387 " --> pdb=" O PHE G 383 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG G 390 " --> pdb=" O ASP G 386 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA G 395 " --> pdb=" O SER G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 429 removed outlier: 3.559A pdb=" N ALA G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE G 421 " --> pdb=" O ALA G 417 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU G 424 " --> pdb=" O SER G 420 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN G 425 " --> pdb=" O ILE G 421 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER G 429 " --> pdb=" O ASN G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 455 removed outlier: 3.865A pdb=" N LEU G 446 " --> pdb=" O ALA G 442 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL G 447 " --> pdb=" O ARG G 443 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE G 448 " --> pdb=" O SER G 444 " (cutoff:3.500A) Proline residue: G 449 - end of helix removed outlier: 3.683A pdb=" N ASN G 455 " --> pdb=" O THR G 451 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 475 removed outlier: 3.633A pdb=" N GLU G 473 " --> pdb=" O ALA G 469 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN G 475 " --> pdb=" O HIS G 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 484 No H-bonds generated for 'chain 'G' and resid 482 through 484' Processing helix chain 'G' and resid 498 through 501 No H-bonds generated for 'chain 'G' and resid 498 through 501' Processing helix chain 'G' and resid 507 through 525 removed outlier: 3.524A pdb=" N ILE G 524 " --> pdb=" O ALA G 520 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 37 removed outlier: 3.678A pdb=" N SER H 24 " --> pdb=" O LYS H 21 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE H 27 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN H 28 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS H 31 " --> pdb=" O ASN H 28 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR H 32 " --> pdb=" O ALA H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 69 removed outlier: 4.783A pdb=" N GLU H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 90 removed outlier: 3.729A pdb=" N SER H 79 " --> pdb=" O PRO H 75 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER H 84 " --> pdb=" O MET H 80 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG H 85 " --> pdb=" O ILE H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 107 Processing helix chain 'H' and resid 110 through 115 removed outlier: 3.973A pdb=" N GLN H 115 " --> pdb=" O HIS H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 119 through 137 removed outlier: 3.522A pdb=" N SER H 124 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 125 " --> pdb=" O VAL H 121 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP H 131 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP H 132 " --> pdb=" O LYS H 128 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER H 135 " --> pdb=" O ASP H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 160 removed outlier: 3.843A pdb=" N ASN H 154 " --> pdb=" O ASP H 150 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE H 156 " --> pdb=" O MET H 152 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER H 159 " --> pdb=" O ILE H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 183 removed outlier: 3.512A pdb=" N SER H 169 " --> pdb=" O SER H 166 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N SER H 170 " --> pdb=" O ARG H 167 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA H 172 " --> pdb=" O SER H 169 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N CYS H 173 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE H 175 " --> pdb=" O ALA H 172 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA H 176 " --> pdb=" O CYS H 173 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU H 177 " --> pdb=" O ASN H 174 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP H 178 " --> pdb=" O ILE H 175 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA H 179 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL H 180 " --> pdb=" O LEU H 177 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N LYS H 181 " --> pdb=" O ASP H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 198 No H-bonds generated for 'chain 'H' and resid 196 through 198' Processing helix chain 'H' and resid 209 through 211 No H-bonds generated for 'chain 'H' and resid 209 through 211' Processing helix chain 'H' and resid 263 through 285 removed outlier: 3.705A pdb=" N GLU H 271 " --> pdb=" O ILE H 267 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N GLU H 272 " --> pdb=" O LEU H 268 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE H 275 " --> pdb=" O GLU H 271 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE H 282 " --> pdb=" O LEU H 278 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLN H 284 " --> pdb=" O GLU H 280 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU H 285 " --> pdb=" O ASP H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 305 removed outlier: 3.522A pdb=" N HIS H 302 " --> pdb=" O ASP H 298 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU H 304 " --> pdb=" O ALA H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 317 through 326 removed outlier: 3.626A pdb=" N ILE H 323 " --> pdb=" O ASP H 319 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA H 324 " --> pdb=" O ASN H 320 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG H 325 " --> pdb=" O ASN H 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 381 through 403 removed outlier: 3.555A pdb=" N GLU H 386 " --> pdb=" O GLU H 382 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLN H 396 " --> pdb=" O GLN H 392 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU H 402 " --> pdb=" O CYS H 398 " (cutoff:3.500A) Processing helix chain 'H' and resid 413 through 423 Processing helix chain 'H' and resid 426 through 428 No H-bonds generated for 'chain 'H' and resid 426 through 428' Processing helix chain 'H' and resid 435 through 453 removed outlier: 3.773A pdb=" N VAL H 440 " --> pdb=" O PRO H 436 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA H 441 " --> pdb=" O TYR H 437 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU H 444 " --> pdb=" O VAL H 440 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N VAL H 446 " --> pdb=" O GLN H 442 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N ILE H 447 " --> pdb=" O ALA H 443 " (cutoff:3.500A) Proline residue: H 448 - end of helix removed outlier: 3.595A pdb=" N LEU H 451 " --> pdb=" O ILE H 447 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE H 452 " --> pdb=" O PRO H 448 " (cutoff:3.500A) Processing helix chain 'H' and resid 462 through 467 Processing helix chain 'H' and resid 469 through 471 No H-bonds generated for 'chain 'H' and resid 469 through 471' Processing helix chain 'H' and resid 490 through 493 No H-bonds generated for 'chain 'H' and resid 490 through 493' Processing helix chain 'H' and resid 499 through 517 removed outlier: 3.546A pdb=" N GLU H 511 " --> pdb=" O LYS H 507 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 7 No H-bonds generated for 'chain 'I' and resid 4 through 7' Processing helix chain 'I' and resid 18 through 37 removed outlier: 3.582A pdb=" N VAL I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASN I 23 " --> pdb=" O ALA I 19 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN I 31 " --> pdb=" O ALA I 27 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL I 33 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N THR I 36 " --> pdb=" O ASP I 32 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASN I 37 " --> pdb=" O VAL I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 64 Processing helix chain 'I' and resid 73 through 85 removed outlier: 4.161A pdb=" N ILE I 77 " --> pdb=" O THR I 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 110 removed outlier: 3.502A pdb=" N LYS I 104 " --> pdb=" O GLY I 100 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU I 108 " --> pdb=" O LYS I 104 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR I 109 " --> pdb=" O GLN I 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 134 removed outlier: 3.574A pdb=" N GLY I 122 " --> pdb=" O ILE I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 154 removed outlier: 3.765A pdb=" N ASP I 150 " --> pdb=" O GLU I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 162 through 178 removed outlier: 3.517A pdb=" N ASP I 166 " --> pdb=" O ALA I 162 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA I 171 " --> pdb=" O VAL I 167 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER I 175 " --> pdb=" O ALA I 171 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 203 No H-bonds generated for 'chain 'I' and resid 201 through 203' Processing helix chain 'I' and resid 253 through 260 removed outlier: 3.790A pdb=" N GLU I 257 " --> pdb=" O ALA I 253 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU I 259 " --> pdb=" O GLU I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 281 removed outlier: 4.061A pdb=" N ARG I 270 " --> pdb=" O PHE I 266 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL I 271 " --> pdb=" O ILE I 267 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE I 274 " --> pdb=" O ARG I 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 301 through 304 No H-bonds generated for 'chain 'I' and resid 301 through 304' Processing helix chain 'I' and resid 318 through 327 removed outlier: 3.786A pdb=" N ARG I 323 " --> pdb=" O ASN I 320 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU I 324 " --> pdb=" O MET I 321 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR I 325 " --> pdb=" O GLU I 322 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU I 326 " --> pdb=" O ARG I 323 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA I 327 " --> pdb=" O LEU I 324 " (cutoff:3.500A) Processing helix chain 'I' and resid 341 through 343 No H-bonds generated for 'chain 'I' and resid 341 through 343' Processing helix chain 'I' and resid 381 through 403 removed outlier: 3.512A pdb=" N THR I 385 " --> pdb=" O LYS I 381 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL I 398 " --> pdb=" O GLY I 394 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA I 401 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 424 removed outlier: 3.595A pdb=" N ILE I 423 " --> pdb=" O ALA I 419 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS I 424 " --> pdb=" O GLU I 420 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 454 removed outlier: 3.865A pdb=" N GLN I 434 " --> pdb=" O GLY I 431 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN I 438 " --> pdb=" O LEU I 435 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU I 444 " --> pdb=" O ALA I 441 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU I 445 " --> pdb=" O ASP I 442 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ILE I 447 " --> pdb=" O LEU I 444 " (cutoff:3.500A) Proline residue: I 448 - end of helix removed outlier: 3.583A pdb=" N LEU I 451 " --> pdb=" O PRO I 448 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN I 454 " --> pdb=" O LEU I 451 " (cutoff:3.500A) Processing helix chain 'I' and resid 459 through 468 removed outlier: 3.946A pdb=" N LEU I 463 " --> pdb=" O LEU I 459 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS I 465 " --> pdb=" O GLU I 461 " (cutoff:3.500A) Processing helix chain 'I' and resid 489 through 491 No H-bonds generated for 'chain 'I' and resid 489 through 491' Processing helix chain 'I' and resid 498 through 517 removed outlier: 3.640A pdb=" N THR I 509 " --> pdb=" O LEU I 505 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL I 510 " --> pdb=" O HIS I 506 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA I 512 " --> pdb=" O CYS I 508 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU I 516 " --> pdb=" O ALA I 512 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU I 517 " --> pdb=" O THR I 513 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 90 through 92 removed outlier: 8.449A pdb=" N VAL A 91 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU A 65 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 9.289A pdb=" N ILE A 64 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N HIS A 6 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL A 66 " --> pdb=" O HIS A 6 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N GLN A 8 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 8.433A pdb=" N VAL A 5 " --> pdb=" O GLN A 131 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N PHE A 133 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE A 7 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU A 135 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ALA A 9 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE A 163 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N LEU A 135 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASN A 165 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 20 through 23 Processing sheet with id= C, first strand: chain 'B' and resid 54 through 57 removed outlier: 3.551A pdb=" N LYS B 54 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 66 " --> pdb=" O LYS B 54 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 202 through 208 removed outlier: 6.770A pdb=" N SER B 373 " --> pdb=" O ARG B 203 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N CYS B 205 " --> pdb=" O SER B 373 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ILE B 375 " --> pdb=" O CYS B 205 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N ILE B 207 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU B 377 " --> pdb=" O ILE B 207 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 239 through 241 removed outlier: 7.031A pdb=" N VAL B 290 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N MET B 311 " --> pdb=" O VAL B 291 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR B 293 " --> pdb=" O MET B 311 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL B 313 " --> pdb=" O THR B 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 349 through 354 Processing sheet with id= G, first strand: chain 'B' and resid 408 through 410 Processing sheet with id= H, first strand: chain 'B' and resid 478 through 480 removed outlier: 4.001A pdb=" N LYS B 490 " --> pdb=" O GLY B 479 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 14 through 17 Processing sheet with id= J, first strand: chain 'C' and resid 47 through 50 removed outlier: 3.551A pdb=" N ILE C 49 " --> pdb=" O THR C 57 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 195 through 201 removed outlier: 7.834A pdb=" N CYS C 370 " --> pdb=" O GLY C 196 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LYS C 198 " --> pdb=" O CYS C 370 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE C 372 " --> pdb=" O LYS C 198 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL C 200 " --> pdb=" O PHE C 372 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU C 374 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR C 371 " --> pdb=" O VAL C 211 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 215 through 217 removed outlier: 3.620A pdb=" N GLU C 349 " --> pdb=" O PHE C 360 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 237 through 240 removed outlier: 6.964A pdb=" N VAL C 288 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU C 240 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N LEU C 290 " --> pdb=" O LEU C 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 405 through 407 Processing sheet with id= O, first strand: chain 'C' and resid 485 through 488 removed outlier: 3.731A pdb=" N ALA C 495 " --> pdb=" O GLY C 486 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP C 493 " --> pdb=" O ASP C 488 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 25 through 28 removed outlier: 3.571A pdb=" N LYS D 535 " --> pdb=" O SER D 26 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= R, first strand: chain 'D' and resid 209 through 213 removed outlier: 6.721A pdb=" N VAL D 383 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N GLU D 212 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE D 385 " --> pdb=" O GLU D 212 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 228 through 230 Processing sheet with id= T, first strand: chain 'D' and resid 248 through 250 removed outlier: 6.805A pdb=" N LEU D 299 " --> pdb=" O ALA D 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'E' and resid 17 through 19 Processing sheet with id= V, first strand: chain 'E' and resid 50 through 53 removed outlier: 3.724A pdb=" N THR E 64 " --> pdb=" O LYS E 50 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 199 through 205 removed outlier: 6.658A pdb=" N CYS E 371 " --> pdb=" O HIS E 200 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ILE E 202 " --> pdb=" O CYS E 371 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE E 373 " --> pdb=" O ILE E 202 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N LYS E 204 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU E 375 " --> pdb=" O LYS E 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'E' and resid 218 through 220 removed outlier: 3.667A pdb=" N ASP E 357 " --> pdb=" O ILE E 354 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 237 through 240 removed outlier: 6.715A pdb=" N CYS E 289 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ALA E 240 " --> pdb=" O CYS E 289 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ILE E 291 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N MET E 310 " --> pdb=" O PHE E 290 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ASN E 292 " --> pdb=" O MET E 310 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE E 312 " --> pdb=" O ASN E 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 406 through 408 Processing sheet with id= AA, first strand: chain 'E' and resid 476 through 478 Processing sheet with id= AB, first strand: chain 'F' and resid 59 through 62 Processing sheet with id= AC, first strand: chain 'F' and resid 208 through 214 removed outlier: 7.005A pdb=" N VAL F 386 " --> pdb=" O LYS F 209 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N VAL F 211 " --> pdb=" O VAL F 386 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE F 388 " --> pdb=" O VAL F 211 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LYS F 213 " --> pdb=" O ILE F 388 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N VAL F 390 " --> pdb=" O LYS F 213 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 387 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU F 222 " --> pdb=" O VAL F 389 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'F' and resid 227 through 229 Processing sheet with id= AE, first strand: chain 'F' and resid 246 through 249 removed outlier: 7.076A pdb=" N VAL F 297 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N ILE F 249 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU F 299 " --> pdb=" O ILE F 249 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N MET F 323 " --> pdb=" O LEU F 298 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ILE F 300 " --> pdb=" O MET F 323 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE F 325 " --> pdb=" O ILE F 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'F' and resid 421 through 423 Processing sheet with id= AG, first strand: chain 'F' and resid 491 through 493 removed outlier: 3.529A pdb=" N SER F 501 " --> pdb=" O GLY F 492 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 9 through 13 Processing sheet with id= AI, first strand: chain 'G' and resid 43 through 46 Processing sheet with id= AJ, first strand: chain 'G' and resid 196 through 201 removed outlier: 3.919A pdb=" N GLY G 379 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER G 374 " --> pdb=" O ILE G 211 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET G 209 " --> pdb=" O ILE G 376 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 213 through 216 removed outlier: 3.553A pdb=" N VAL G 352 " --> pdb=" O LEU G 363 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU G 350 " --> pdb=" O LYS G 365 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'G' and resid 346 through 348 removed outlier: 3.521A pdb=" N ALA G 348 " --> pdb=" O ALA G 232 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA G 232 " --> pdb=" O ALA G 348 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL G 285 " --> pdb=" O ALA G 235 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU G 237 " --> pdb=" O VAL G 285 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU G 287 " --> pdb=" O LEU G 237 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N MET G 306 " --> pdb=" O ILE G 286 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N THR G 288 " --> pdb=" O MET G 306 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL G 308 " --> pdb=" O THR G 288 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 408 through 410 Processing sheet with id= AN, first strand: chain 'H' and resid 15 through 18 Processing sheet with id= AO, first strand: chain 'H' and resid 199 through 204 removed outlier: 6.776A pdb=" N CYS H 372 " --> pdb=" O ARG H 200 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLU H 202 " --> pdb=" O CYS H 372 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE H 374 " --> pdb=" O GLU H 202 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N ILE H 204 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU H 376 " --> pdb=" O ILE H 204 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR H 373 " --> pdb=" O LEU H 215 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS H 213 " --> pdb=" O LEU H 375 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 218 through 220 Processing sheet with id= AQ, first strand: chain 'H' and resid 238 through 241 removed outlier: 6.539A pdb=" N VAL H 289 " --> pdb=" O VAL H 239 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LEU H 241 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE H 291 " --> pdb=" O LEU H 241 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR H 310 " --> pdb=" O VAL H 290 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N THR H 292 " --> pdb=" O THR H 310 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE H 312 " --> pdb=" O THR H 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AQ Processing sheet with id= AR, first strand: chain 'H' and resid 407 through 409 Processing sheet with id= AS, first strand: chain 'H' and resid 478 through 480 Processing sheet with id= AT, first strand: chain 'I' and resid 45 through 48 removed outlier: 3.684A pdb=" N LYS I 45 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N THR I 57 " --> pdb=" O LYS I 45 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'I' and resid 192 through 196 Processing sheet with id= AV, first strand: chain 'I' and resid 210 through 212 removed outlier: 3.560A pdb=" N TYR I 351 " --> pdb=" O PHE I 362 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU I 349 " --> pdb=" O GLU I 364 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'I' and resid 228 through 233 removed outlier: 7.117A pdb=" N GLY I 288 " --> pdb=" O TYR I 229 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N LEU I 231 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL I 290 " --> pdb=" O LEU I 231 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N CYS I 233 " --> pdb=" O VAL I 290 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE I 292 " --> pdb=" O CYS I 233 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL I 311 " --> pdb=" O PHE I 289 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'I' and resid 407 through 409 removed outlier: 3.515A pdb=" N VAL I 408 " --> pdb=" O ASP I 496 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'I' and resid 477 through 479 1203 hydrogen bonds defined for protein. 3321 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: 12.61 Time building geometry restraints manager: 14.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 6030 1.28 - 1.41: 7278 1.41 - 1.55: 21254 1.55 - 1.68: 48 1.68 - 1.81: 361 Bond restraints: 34971 Sorted by residual: bond pdb=" F1 AF3 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F1 AF3 C 603 " pdb="AL AF3 C 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F2 AF3 B 601 " pdb="AL AF3 B 601 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.801 -0.164 2.00e-02 2.50e+03 6.69e+01 bond pdb=" F1 AF3 I 603 " pdb="AL AF3 I 603 " ideal model delta sigma weight residual 1.637 1.800 -0.163 2.00e-02 2.50e+03 6.68e+01 ... (remaining 34966 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.59: 814 106.59 - 114.02: 21142 114.02 - 121.46: 16741 121.46 - 128.89: 8374 128.89 - 136.32: 155 Bond angle restraints: 47226 Sorted by residual: angle pdb=" N SER F 181 " pdb=" CA SER F 181 " pdb=" C SER F 181 " ideal model delta sigma weight residual 113.02 103.87 9.15 1.20e+00 6.94e-01 5.81e+01 angle pdb=" N GLU D 444 " pdb=" CA GLU D 444 " pdb=" C GLU D 444 " ideal model delta sigma weight residual 114.31 104.97 9.34 1.29e+00 6.01e-01 5.25e+01 angle pdb=" C THR D 252 " pdb=" N CYS D 253 " pdb=" CA CYS D 253 " ideal model delta sigma weight residual 120.68 131.64 -10.96 1.52e+00 4.33e-01 5.20e+01 angle pdb=" N LEU F 117 " pdb=" CA LEU F 117 " pdb=" C LEU F 117 " ideal model delta sigma weight residual 111.82 104.81 7.01 1.16e+00 7.43e-01 3.65e+01 angle pdb=" C GLU D 444 " pdb=" N GLN D 445 " pdb=" CA GLN D 445 " ideal model delta sigma weight residual 120.28 112.16 8.12 1.44e+00 4.82e-01 3.18e+01 ... (remaining 47221 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.09: 20792 34.09 - 68.17: 729 68.17 - 102.26: 44 102.26 - 136.34: 1 136.34 - 170.43: 6 Dihedral angle restraints: 21572 sinusoidal: 8687 harmonic: 12885 Sorted by residual: dihedral pdb=" C5' ADP C 602 " pdb=" O5' ADP C 602 " pdb=" PA ADP C 602 " pdb=" O2A ADP C 602 " ideal model delta sinusoidal sigma weight residual -60.00 110.43 -170.43 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP C 602 " pdb=" O3A ADP C 602 " pdb=" PA ADP C 602 " pdb=" PB ADP C 602 " ideal model delta sinusoidal sigma weight residual -60.00 102.40 -162.40 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" O1B ADP B 603 " pdb=" O3A ADP B 603 " pdb=" PB ADP B 603 " pdb=" PA ADP B 603 " ideal model delta sinusoidal sigma weight residual 300.00 148.61 151.39 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 21569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 5237 0.089 - 0.178: 351 0.178 - 0.267: 9 0.267 - 0.356: 3 0.356 - 0.445: 1 Chirality restraints: 5601 Sorted by residual: chirality pdb=" CB VAL I 160 " pdb=" CA VAL I 160 " pdb=" CG1 VAL I 160 " pdb=" CG2 VAL I 160 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 4.96e+00 chirality pdb=" CA SER E 168 " pdb=" N SER E 168 " pdb=" C SER E 168 " pdb=" CB SER E 168 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA ASP C 61 " pdb=" N ASP C 61 " pdb=" C ASP C 61 " pdb=" CB ASP C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.41e+00 ... (remaining 5598 not shown) Planarity restraints: 6039 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO D 441 " -0.027 2.00e-02 2.50e+03 5.09e-02 2.59e+01 pdb=" C PRO D 441 " 0.088 2.00e-02 2.50e+03 pdb=" O PRO D 441 " -0.032 2.00e-02 2.50e+03 pdb=" N THR D 442 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN G 187 " -0.079 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO G 188 " 0.201 5.00e-02 4.00e+02 pdb=" CA PRO G 188 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO G 188 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 178 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C GLN F 178 " 0.077 2.00e-02 2.50e+03 pdb=" O GLN F 178 " -0.029 2.00e-02 2.50e+03 pdb=" N TYR F 179 " -0.026 2.00e-02 2.50e+03 ... (remaining 6036 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 143 2.48 - 3.08: 21650 3.08 - 3.69: 48676 3.69 - 4.29: 71020 4.29 - 4.90: 120512 Nonbonded interactions: 262001 Sorted by model distance: nonbonded pdb="MG MG E 601 " pdb=" F1 AF3 E 603 " model vdw 1.873 2.120 nonbonded pdb="MG MG D 601 " pdb=" O1B ADP D 602 " model vdw 1.913 2.170 nonbonded pdb=" OD1 ASP C 92 " pdb="MG MG C 601 " model vdw 1.914 2.170 nonbonded pdb="MG MG H 601 " pdb=" F1 AF3 H 603 " model vdw 1.950 2.120 nonbonded pdb="MG MG C 601 " pdb=" O1A ADP C 602 " model vdw 1.968 2.170 ... (remaining 261996 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.010 Check model and map are aligned: 0.500 Set scattering table: 0.330 Process input model: 92.290 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.130 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 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 0.164 34971 Z= 0.332 Angle : 0.681 10.959 47226 Z= 0.402 Chirality : 0.044 0.445 5601 Planarity : 0.004 0.116 6039 Dihedral : 16.384 170.425 13232 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.14 % Favored : 96.75 % Rotamer: Outliers : 0.48 % Allowed : 17.50 % Favored : 82.02 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.11), residues: 4455 helix: -2.46 (0.09), residues: 2082 sheet: -0.94 (0.23), residues: 542 loop : -1.58 (0.13), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 319 HIS 0.008 0.001 HIS I 71 PHE 0.017 0.001 PHE H 185 TYR 0.027 0.001 TYR F 179 ARG 0.005 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 245 time to evaluate : 4.411 Fit side-chains revert: symmetry clash REVERT: A 379 LYS cc_start: 0.8463 (mmtp) cc_final: 0.7527 (ptmt) REVERT: C 123 ARG cc_start: 0.8411 (mtp85) cc_final: 0.7934 (ttp-110) REVERT: F 60 MET cc_start: 0.8982 (tmm) cc_final: 0.8582 (ppp) REVERT: F 343 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7792 (mmmt) REVERT: F 458 MET cc_start: 0.8979 (mmp) cc_final: 0.8605 (mmt) REVERT: G 171 MET cc_start: 0.8244 (mtp) cc_final: 0.7520 (ttm) REVERT: I 190 MET cc_start: 0.8119 (mmp) cc_final: 0.7891 (mmt) REVERT: I 418 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8317 (mtt) outliers start: 18 outliers final: 3 residues processed: 260 average time/residue: 0.4371 time to fit residues: 192.1073 Evaluate side-chains 229 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 225 time to evaluate : 4.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 418 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 374 optimal weight: 10.0000 chunk 335 optimal weight: 6.9990 chunk 186 optimal weight: 9.9990 chunk 114 optimal weight: 9.9990 chunk 226 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 347 optimal weight: 6.9990 chunk 134 optimal weight: 0.4980 chunk 211 optimal weight: 5.9990 chunk 258 optimal weight: 8.9990 chunk 402 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 HIS ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 278 GLN H 390 ASN ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34971 Z= 0.265 Angle : 0.587 7.923 47226 Z= 0.295 Chirality : 0.043 0.163 5601 Planarity : 0.004 0.070 6039 Dihedral : 7.420 157.909 4855 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.61 % Favored : 96.27 % Rotamer: Outliers : 1.71 % Allowed : 16.22 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.12), residues: 4455 helix: -0.93 (0.11), residues: 2072 sheet: -0.82 (0.22), residues: 581 loop : -1.48 (0.13), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 271 HIS 0.011 0.001 HIS I 71 PHE 0.015 0.001 PHE H 185 TYR 0.016 0.001 TYR F 282 ARG 0.003 0.000 ARG E 89 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 230 time to evaluate : 4.219 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8223 (mp) REVERT: A 379 LYS cc_start: 0.8406 (mmtp) cc_final: 0.7552 (ptmt) REVERT: B 319 TRP cc_start: 0.7073 (m-90) cc_final: 0.6843 (m-90) REVERT: C 123 ARG cc_start: 0.8201 (mtp85) cc_final: 0.7758 (ttp-110) REVERT: G 44 MET cc_start: 0.8258 (ttm) cc_final: 0.8007 (ttp) REVERT: I 121 GLU cc_start: 0.8625 (OUTLIER) cc_final: 0.7779 (mp0) REVERT: I 190 MET cc_start: 0.8119 (mmp) cc_final: 0.7854 (mmt) REVERT: I 238 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7545 (mt-10) outliers start: 64 outliers final: 35 residues processed: 285 average time/residue: 0.4320 time to fit residues: 210.0180 Evaluate side-chains 262 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 225 time to evaluate : 4.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 60 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 183 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 223 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 chunk 334 optimal weight: 4.9990 chunk 273 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 403 optimal weight: 0.6980 chunk 435 optimal weight: 5.9990 chunk 358 optimal weight: 9.9990 chunk 399 optimal weight: 10.0000 chunk 137 optimal weight: 9.9990 chunk 323 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 411 ASN F 296 ASN ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 34971 Z= 0.304 Angle : 0.582 7.976 47226 Z= 0.288 Chirality : 0.044 0.163 5601 Planarity : 0.003 0.053 6039 Dihedral : 7.246 150.381 4851 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.70 % Favored : 96.18 % Rotamer: Outliers : 2.62 % Allowed : 16.30 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.12), residues: 4455 helix: -0.40 (0.11), residues: 2082 sheet: -0.81 (0.22), residues: 600 loop : -1.47 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 324 HIS 0.014 0.001 HIS A 190 PHE 0.015 0.001 PHE H 185 TYR 0.014 0.001 TYR F 282 ARG 0.004 0.000 ARG F 435 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 231 time to evaluate : 4.129 Fit side-chains REVERT: A 139 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8267 (mp) REVERT: A 379 LYS cc_start: 0.8355 (mmtp) cc_final: 0.7508 (ptpt) REVERT: B 168 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.8978 (mp) REVERT: B 319 TRP cc_start: 0.7911 (m-90) cc_final: 0.7524 (m-90) REVERT: B 464 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8339 (mp) REVERT: C 123 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7733 (ttp-110) REVERT: C 130 GLN cc_start: 0.8462 (mt0) cc_final: 0.8192 (mt0) REVERT: F 395 LYS cc_start: 0.7847 (ptpt) cc_final: 0.7418 (tptp) REVERT: G 44 MET cc_start: 0.8338 (ttm) cc_final: 0.8138 (ttp) REVERT: I 121 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: I 221 MET cc_start: 0.8834 (mtt) cc_final: 0.8490 (mtp) REVERT: I 238 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7730 (mt-10) REVERT: I 418 MET cc_start: 0.8588 (mtm) cc_final: 0.8248 (mtm) outliers start: 98 outliers final: 53 residues processed: 320 average time/residue: 0.4302 time to fit residues: 234.3594 Evaluate side-chains 277 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 220 time to evaluate : 4.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain E residue 379 THR Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 398 optimal weight: 1.9990 chunk 303 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 44 optimal weight: 0.0070 chunk 192 optimal weight: 6.9990 chunk 270 optimal weight: 6.9990 chunk 404 optimal weight: 5.9990 chunk 428 optimal weight: 5.9990 chunk 211 optimal weight: 0.8980 chunk 383 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 overall best weight: 2.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN C 511 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34971 Z= 0.220 Angle : 0.529 8.988 47226 Z= 0.258 Chirality : 0.042 0.158 5601 Planarity : 0.003 0.045 6039 Dihedral : 6.972 147.714 4851 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.50 % Favored : 96.39 % Rotamer: Outliers : 2.40 % Allowed : 17.10 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.12), residues: 4455 helix: -0.02 (0.12), residues: 2083 sheet: -0.67 (0.22), residues: 604 loop : -1.42 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 324 HIS 0.006 0.001 HIS I 71 PHE 0.016 0.001 PHE A 81 TYR 0.014 0.001 TYR I 250 ARG 0.002 0.000 ARG H 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 238 time to evaluate : 4.392 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 267 MET cc_start: 0.7042 (ppp) cc_final: 0.5457 (ptp) REVERT: A 379 LYS cc_start: 0.8363 (mmtp) cc_final: 0.7482 (ptpt) REVERT: B 168 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8886 (mp) REVERT: B 319 TRP cc_start: 0.8084 (m-90) cc_final: 0.7615 (m-90) REVERT: B 464 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8320 (mp) REVERT: C 123 ARG cc_start: 0.8071 (mtp85) cc_final: 0.7657 (ttp-110) REVERT: C 130 GLN cc_start: 0.8450 (mt0) cc_final: 0.8205 (mt0) REVERT: E 275 MET cc_start: 0.8650 (tpp) cc_final: 0.8271 (tpp) REVERT: F 343 LYS cc_start: 0.8347 (mmtt) cc_final: 0.7919 (mtmm) REVERT: F 395 LYS cc_start: 0.7722 (ptpt) cc_final: 0.7342 (tptp) REVERT: F 456 ASP cc_start: 0.7486 (t0) cc_final: 0.7267 (t0) REVERT: I 221 MET cc_start: 0.8885 (mtt) cc_final: 0.8540 (mtp) outliers start: 90 outliers final: 54 residues processed: 316 average time/residue: 0.4222 time to fit residues: 226.4730 Evaluate side-chains 277 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 220 time to evaluate : 4.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 224 ILE Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 181 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 356 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 chunk 6 optimal weight: 9.9990 chunk 318 optimal weight: 10.0000 chunk 176 optimal weight: 0.7980 chunk 365 optimal weight: 7.9990 chunk 295 optimal weight: 0.0270 chunk 0 optimal weight: 10.0000 chunk 218 optimal weight: 10.0000 chunk 384 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 overall best weight: 3.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 267 ASN C 511 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN H 390 ASN ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 294 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 34971 Z= 0.272 Angle : 0.552 8.874 47226 Z= 0.270 Chirality : 0.043 0.157 5601 Planarity : 0.003 0.042 6039 Dihedral : 6.970 144.855 4851 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.97 % Favored : 95.91 % Rotamer: Outliers : 3.13 % Allowed : 17.23 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.12), residues: 4455 helix: 0.09 (0.12), residues: 2098 sheet: -0.63 (0.22), residues: 594 loop : -1.46 (0.14), residues: 1763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 324 HIS 0.007 0.001 HIS A 396 PHE 0.016 0.001 PHE A 81 TYR 0.013 0.001 TYR F 282 ARG 0.006 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 229 time to evaluate : 4.056 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8283 (mp) REVERT: A 267 MET cc_start: 0.7125 (ppp) cc_final: 0.5665 (ptp) REVERT: A 379 LYS cc_start: 0.8370 (mmtp) cc_final: 0.7478 (ptpt) REVERT: B 168 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.8858 (mp) REVERT: B 464 ILE cc_start: 0.8785 (OUTLIER) cc_final: 0.8316 (mp) REVERT: C 49 ILE cc_start: 0.8356 (OUTLIER) cc_final: 0.8063 (mp) REVERT: C 123 ARG cc_start: 0.8101 (mtp85) cc_final: 0.7678 (ttp-110) REVERT: C 130 GLN cc_start: 0.8428 (mt0) cc_final: 0.8180 (mt0) REVERT: D 170 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8646 (mtpp) REVERT: E 275 MET cc_start: 0.8666 (tpp) cc_final: 0.8297 (tpp) REVERT: F 301 GLN cc_start: 0.8987 (OUTLIER) cc_final: 0.8541 (tt0) REVERT: F 343 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7974 (mtmm) REVERT: F 395 LYS cc_start: 0.7824 (ptpt) cc_final: 0.7362 (tptp) REVERT: F 484 HIS cc_start: 0.8802 (OUTLIER) cc_final: 0.8378 (t70) REVERT: H 331 ILE cc_start: 0.8832 (mm) cc_final: 0.8486 (mm) REVERT: I 221 MET cc_start: 0.8906 (mtt) cc_final: 0.8562 (mtp) outliers start: 117 outliers final: 82 residues processed: 335 average time/residue: 0.4106 time to fit residues: 234.2388 Evaluate side-chains 307 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 218 time to evaluate : 3.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 353 ILE Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 433 LEU Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 184 GLN Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 484 HIS Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 425 ASN Chi-restraints excluded: chain G residue 528 ASP Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 196 LYS Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 183 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 144 optimal weight: 2.9990 chunk 385 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 428 optimal weight: 9.9990 chunk 355 optimal weight: 7.9990 chunk 198 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 141 optimal weight: 0.0770 chunk 225 optimal weight: 4.9990 overall best weight: 3.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 366 ASN G 205 GLN ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 34971 Z= 0.220 Angle : 0.526 8.820 47226 Z= 0.255 Chirality : 0.042 0.155 5601 Planarity : 0.003 0.040 6039 Dihedral : 6.844 146.881 4850 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 2.67 % Allowed : 17.85 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4455 helix: 0.28 (0.12), residues: 2095 sheet: -0.57 (0.22), residues: 596 loop : -1.39 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP I 495 HIS 0.012 0.001 HIS I 71 PHE 0.013 0.001 PHE H 185 TYR 0.013 0.001 TYR I 250 ARG 0.005 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 231 time to evaluate : 4.161 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8292 (mp) REVERT: A 267 MET cc_start: 0.7249 (ppp) cc_final: 0.5835 (ptp) REVERT: A 379 LYS cc_start: 0.8356 (mmtp) cc_final: 0.7416 (ptpt) REVERT: B 464 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8321 (mp) REVERT: C 49 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8136 (mp) REVERT: C 123 ARG cc_start: 0.8060 (mtp85) cc_final: 0.7647 (ttp-110) REVERT: C 130 GLN cc_start: 0.8400 (mt0) cc_final: 0.8138 (mt0) REVERT: D 170 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8625 (mtpp) REVERT: E 275 MET cc_start: 0.8674 (tpp) cc_final: 0.8325 (tpp) REVERT: F 301 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8540 (tt0) REVERT: F 343 LYS cc_start: 0.8375 (mmtt) cc_final: 0.7970 (mtmm) REVERT: F 395 LYS cc_start: 0.7800 (ptpt) cc_final: 0.7353 (tptp) REVERT: F 484 HIS cc_start: 0.8868 (OUTLIER) cc_final: 0.8400 (t70) REVERT: I 221 MET cc_start: 0.8919 (mtt) cc_final: 0.8564 (mtp) outliers start: 100 outliers final: 73 residues processed: 322 average time/residue: 0.4152 time to fit residues: 233.4216 Evaluate side-chains 297 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 218 time to evaluate : 3.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 182 HIS Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 484 HIS Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 528 ASP Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 183 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 244 VAL Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 413 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 244 optimal weight: 7.9990 chunk 313 optimal weight: 0.0670 chunk 242 optimal weight: 4.9990 chunk 360 optimal weight: 0.8980 chunk 239 optimal weight: 10.0000 chunk 426 optimal weight: 9.9990 chunk 267 optimal weight: 10.0000 chunk 260 optimal weight: 1.9990 chunk 197 optimal weight: 2.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 353 GLN ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34971 Z= 0.174 Angle : 0.506 9.512 47226 Z= 0.243 Chirality : 0.042 0.160 5601 Planarity : 0.003 0.039 6039 Dihedral : 6.665 145.145 4850 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.55 % Favored : 96.34 % Rotamer: Outliers : 2.64 % Allowed : 18.17 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.13), residues: 4455 helix: 0.50 (0.12), residues: 2089 sheet: -0.42 (0.22), residues: 606 loop : -1.31 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP I 495 HIS 0.007 0.001 HIS I 71 PHE 0.012 0.001 PHE H 185 TYR 0.012 0.001 TYR I 250 ARG 0.004 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 233 time to evaluate : 4.182 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8291 (mp) REVERT: A 267 MET cc_start: 0.7198 (ppp) cc_final: 0.5836 (ptp) REVERT: A 379 LYS cc_start: 0.8369 (mmtp) cc_final: 0.7395 (ptpt) REVERT: B 168 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.8810 (mp) REVERT: B 464 ILE cc_start: 0.8793 (OUTLIER) cc_final: 0.8298 (mp) REVERT: C 49 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8086 (mp) REVERT: C 130 GLN cc_start: 0.8371 (mt0) cc_final: 0.8105 (mt0) REVERT: D 170 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8612 (mtpp) REVERT: E 275 MET cc_start: 0.8669 (tpp) cc_final: 0.8353 (tpp) REVERT: F 261 ASP cc_start: 0.8334 (OUTLIER) cc_final: 0.8086 (p0) REVERT: F 301 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: F 343 LYS cc_start: 0.8370 (mmtt) cc_final: 0.7943 (mtmm) REVERT: F 395 LYS cc_start: 0.7785 (ptpt) cc_final: 0.7325 (pttm) REVERT: F 414 CYS cc_start: 0.8378 (m) cc_final: 0.7921 (m) REVERT: F 484 HIS cc_start: 0.8851 (OUTLIER) cc_final: 0.8334 (t70) REVERT: G 171 MET cc_start: 0.8172 (mtp) cc_final: 0.7726 (ttm) REVERT: G 228 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.7510 (ttt-90) REVERT: I 221 MET cc_start: 0.8919 (mtt) cc_final: 0.8551 (mtp) outliers start: 99 outliers final: 70 residues processed: 322 average time/residue: 0.4083 time to fit residues: 224.2562 Evaluate side-chains 296 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 217 time to evaluate : 3.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 54 LYS Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 372 LEU Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 261 ASP Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 484 HIS Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 228 ARG Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 528 ASP Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 183 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 264 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 271 optimal weight: 10.0000 chunk 290 optimal weight: 6.9990 chunk 211 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 335 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 34971 Z= 0.317 Angle : 0.576 8.111 47226 Z= 0.281 Chirality : 0.044 0.155 5601 Planarity : 0.003 0.038 6039 Dihedral : 6.916 145.465 4850 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.29 % Favored : 95.60 % Rotamer: Outliers : 2.83 % Allowed : 18.30 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4455 helix: 0.40 (0.12), residues: 2101 sheet: -0.60 (0.23), residues: 581 loop : -1.38 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 324 HIS 0.007 0.001 HIS I 71 PHE 0.014 0.001 PHE H 185 TYR 0.012 0.001 TYR I 250 ARG 0.003 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 218 time to evaluate : 4.533 Fit side-chains REVERT: A 139 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8329 (mp) REVERT: A 267 MET cc_start: 0.7185 (ppp) cc_final: 0.5838 (ptp) REVERT: B 168 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.8845 (mp) REVERT: B 464 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8265 (mp) REVERT: C 49 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8098 (mp) REVERT: C 130 GLN cc_start: 0.8412 (mt0) cc_final: 0.8138 (mt0) REVERT: D 170 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8459 (mtmm) REVERT: E 275 MET cc_start: 0.8684 (tpp) cc_final: 0.8338 (tpp) REVERT: F 301 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: F 343 LYS cc_start: 0.8405 (mmmt) cc_final: 0.8057 (mtmm) REVERT: F 395 LYS cc_start: 0.7856 (ptpt) cc_final: 0.7387 (tptp) REVERT: F 484 HIS cc_start: 0.8903 (OUTLIER) cc_final: 0.8340 (t70) REVERT: G 228 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7584 (ttt-90) REVERT: H 331 ILE cc_start: 0.8860 (mm) cc_final: 0.8551 (mm) REVERT: I 121 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: I 221 MET cc_start: 0.8922 (mtt) cc_final: 0.8555 (mtp) outliers start: 106 outliers final: 80 residues processed: 313 average time/residue: 0.4067 time to fit residues: 219.9292 Evaluate side-chains 304 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 215 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 ILE Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 312 LEU Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 49 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 249 GLU Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 456 ASP Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 330 GLU Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain F residue 36 SER Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 253 LEU Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 374 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 484 HIS Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain G residue 146 ASP Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 228 ARG Chi-restraints excluded: chain G residue 231 ASN Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 LEU Chi-restraints excluded: chain G residue 352 VAL Chi-restraints excluded: chain G residue 528 ASP Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 165 ILE Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain I residue 57 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 183 ASP Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 373 THR Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 388 optimal weight: 1.9990 chunk 409 optimal weight: 0.9990 chunk 373 optimal weight: 0.9990 chunk 397 optimal weight: 8.9990 chunk 408 optimal weight: 5.9990 chunk 239 optimal weight: 9.9990 chunk 173 optimal weight: 0.0370 chunk 312 optimal weight: 10.0000 chunk 122 optimal weight: 0.9990 chunk 359 optimal weight: 2.9990 chunk 376 optimal weight: 6.9990 overall best weight: 1.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 34971 Z= 0.126 Angle : 0.490 8.758 47226 Z= 0.235 Chirality : 0.041 0.202 5601 Planarity : 0.003 0.037 6039 Dihedral : 6.491 143.653 4850 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 1.66 % Allowed : 19.58 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.13), residues: 4455 helix: 0.76 (0.12), residues: 2096 sheet: -0.38 (0.22), residues: 599 loop : -1.18 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 435 HIS 0.006 0.001 HIS I 71 PHE 0.010 0.001 PHE H 185 TYR 0.014 0.001 TYR I 250 ARG 0.003 0.000 ARG I 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 235 time to evaluate : 4.333 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8292 (mp) REVERT: A 267 MET cc_start: 0.6814 (ppp) cc_final: 0.5800 (ptp) REVERT: A 379 LYS cc_start: 0.8365 (mmtp) cc_final: 0.7401 (ptpt) REVERT: B 168 ILE cc_start: 0.9276 (OUTLIER) cc_final: 0.8730 (mp) REVERT: B 464 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8273 (mp) REVERT: C 130 GLN cc_start: 0.8328 (mt0) cc_final: 0.8071 (mt0) REVERT: D 170 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8602 (mtpp) REVERT: F 301 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8497 (tt0) REVERT: F 343 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7924 (mtmm) REVERT: F 395 LYS cc_start: 0.7775 (ptpt) cc_final: 0.7324 (pttm) REVERT: F 484 HIS cc_start: 0.8823 (OUTLIER) cc_final: 0.8207 (t70) REVERT: G 171 MET cc_start: 0.8095 (mtp) cc_final: 0.7813 (ttm) REVERT: I 221 MET cc_start: 0.8938 (mtt) cc_final: 0.8576 (mtp) outliers start: 62 outliers final: 47 residues processed: 291 average time/residue: 0.4322 time to fit residues: 215.5169 Evaluate side-chains 274 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 221 time to evaluate : 4.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 484 HIS Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 528 ASP Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 333 LEU Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 396 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 420 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 chunk 292 optimal weight: 4.9990 chunk 441 optimal weight: 0.9980 chunk 406 optimal weight: 6.9990 chunk 351 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 271 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 289 GLN ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 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 0.038 34971 Z= 0.197 Angle : 0.519 10.273 47226 Z= 0.248 Chirality : 0.042 0.234 5601 Planarity : 0.003 0.037 6039 Dihedral : 6.550 141.530 4850 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 1.74 % Allowed : 19.61 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.13), residues: 4455 helix: 0.83 (0.12), residues: 2098 sheet: -0.36 (0.22), residues: 599 loop : -1.19 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 324 HIS 0.005 0.001 HIS I 71 PHE 0.012 0.001 PHE H 185 TYR 0.012 0.001 TYR F 282 ARG 0.004 0.000 ARG I 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 220 time to evaluate : 4.179 Fit side-chains revert: symmetry clash REVERT: A 139 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8309 (mp) REVERT: A 267 MET cc_start: 0.6875 (ppp) cc_final: 0.5879 (ptp) REVERT: A 374 ILE cc_start: 0.6501 (OUTLIER) cc_final: 0.6295 (tt) REVERT: B 168 ILE cc_start: 0.9272 (OUTLIER) cc_final: 0.8757 (mp) REVERT: B 464 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8300 (mp) REVERT: C 130 GLN cc_start: 0.8347 (mt0) cc_final: 0.8078 (mt0) REVERT: D 170 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8621 (mtpp) REVERT: F 301 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: F 343 LYS cc_start: 0.8315 (mmmt) cc_final: 0.7967 (mtmm) REVERT: F 395 LYS cc_start: 0.7831 (ptpt) cc_final: 0.7371 (pttm) REVERT: F 484 HIS cc_start: 0.8857 (OUTLIER) cc_final: 0.8249 (t70) REVERT: H 49 MET cc_start: 0.8749 (ptp) cc_final: 0.8526 (mtp) REVERT: H 331 ILE cc_start: 0.8717 (mm) cc_final: 0.8402 (mm) REVERT: I 221 MET cc_start: 0.8920 (mtt) cc_final: 0.8546 (mtp) outliers start: 65 outliers final: 52 residues processed: 279 average time/residue: 0.4121 time to fit residues: 199.0946 Evaluate side-chains 279 residues out of total 3743 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 220 time to evaluate : 4.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 37 HIS Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 190 HIS Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain B residue 95 GLN Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 205 CYS Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 299 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain C residue 39 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 120 ILE Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 405 VAL Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 487 VAL Chi-restraints excluded: chain D residue 32 GLU Chi-restraints excluded: chain D residue 170 LYS Chi-restraints excluded: chain D residue 366 THR Chi-restraints excluded: chain D residue 413 ILE Chi-restraints excluded: chain D residue 444 GLU Chi-restraints excluded: chain D residue 526 MET Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 87 MET Chi-restraints excluded: chain E residue 144 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 341 VAL Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 119 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 184 SER Chi-restraints excluded: chain F residue 272 MET Chi-restraints excluded: chain F residue 273 ASP Chi-restraints excluded: chain F residue 289 GLN Chi-restraints excluded: chain F residue 301 GLN Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 484 HIS Chi-restraints excluded: chain F residue 508 VAL Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 528 ASP Chi-restraints excluded: chain H residue 59 MET Chi-restraints excluded: chain H residue 433 GLU Chi-restraints excluded: chain H residue 459 THR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 404 ASP Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 479 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 443 random chunks: chunk 215 optimal weight: 7.9990 chunk 279 optimal weight: 1.9990 chunk 374 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 324 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 352 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 361 optimal weight: 9.9990 chunk 44 optimal weight: 0.0010 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 ASN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.079807 restraints weight = 72221.984| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.46 r_work: 0.3054 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.152 34971 Z= 0.199 Angle : 0.627 59.093 47226 Z= 0.329 Chirality : 0.043 0.818 5601 Planarity : 0.003 0.036 6039 Dihedral : 6.560 141.493 4850 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.64 % Favored : 96.25 % Rotamer: Outliers : 1.82 % Allowed : 19.42 % Favored : 78.76 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4455 helix: 0.84 (0.12), residues: 2098 sheet: -0.38 (0.22), residues: 604 loop : -1.18 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 324 HIS 0.005 0.001 HIS I 71 PHE 0.011 0.001 PHE H 185 TYR 0.012 0.001 TYR F 282 ARG 0.003 0.000 ARG I 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6477.31 seconds wall clock time: 119 minutes 13.45 seconds (7153.45 seconds total)