Starting phenix.real_space_refine on Sun Mar 24 17:31:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jal_6350/03_2024/3jal_6350_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jal_6350/03_2024/3jal_6350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jal_6350/03_2024/3jal_6350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jal_6350/03_2024/3jal_6350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jal_6350/03_2024/3jal_6350_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jal_6350/03_2024/3jal_6350_updated.pdb" } resolution = 3.5 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= -0.010 sd= 0.921 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 6 5.21 5 S 290 5.16 5 C 27078 2.51 5 N 7340 2.21 5 O 8268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 3": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E ARG 64": "NH1" <-> "NH2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ARG 390": "NH1" <-> "NH2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "F GLU 47": "OE1" <-> "OE2" Residue "N GLU 13": "OE1" <-> "OE2" Residue "J GLU 3": "OE1" <-> "OE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J GLU 254": "OE1" <-> "OE2" Residue "J GLU 279": "OE1" <-> "OE2" Residue "J ARG 390": "NH1" <-> "NH2" Residue "J TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 415": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C GLU 55": "OE1" <-> "OE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C GLU 254": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C ARG 390": "NH1" <-> "NH2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "L GLU 3": "OE1" <-> "OE2" Residue "L GLU 55": "OE1" <-> "OE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L GLU 254": "OE1" <-> "OE2" Residue "L GLU 279": "OE1" <-> "OE2" Residue "L ARG 390": "NH1" <-> "NH2" Residue "L GLU 415": "OE1" <-> "OE2" Residue "I GLU 47": "OE1" <-> "OE2" Residue "A GLU 3": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ARG 390": "NH1" <-> "NH2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "B GLU 47": "OE1" <-> "OE2" Residue "M GLU 13": "OE1" <-> "OE2" Residue "K GLU 3": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K GLU 254": "OE1" <-> "OE2" Residue "K GLU 279": "OE1" <-> "OE2" Residue "K ARG 390": "NH1" <-> "NH2" Residue "K GLU 415": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43012 Number of models: 1 Model: "" Number of chains: 26 Chain: "E" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "J" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "C" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "L" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 127} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "K" Number of atoms: 3380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3380 Classifications: {'peptide': 432} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 3368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3368 Classifications: {'peptide': 429} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 408} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'G2P': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 21.55, per 1000 atoms: 0.50 Number of scatterers: 43012 At special positions: 0 Unit cell: (172.92, 112.2, 212.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 290 16.00 P 30 15.00 Mg 6 11.99 O 8268 8.00 N 7340 7.00 C 27078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.46 Conformation dependent library (CDL) restraints added in 7.3 seconds 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10080 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 262 helices and 30 sheets defined 49.5% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.67 Creating SS restraints... Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 49 through 51 No H-bonds generated for 'chain 'E' and resid 49 through 51' Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.633A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 103 through 107 Processing helix chain 'E' and resid 111 through 113 No H-bonds generated for 'chain 'E' and resid 111 through 113' Processing helix chain 'E' and resid 115 through 128 removed outlier: 3.617A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 160 removed outlier: 4.080A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.555A pdb=" N LEU E 189 " --> pdb=" O ASN E 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR E 190 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR E 194 " --> pdb=" O THR E 191 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU E 195 " --> pdb=" O HIS E 192 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU E 196 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.481A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 removed outlier: 3.921A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR E 257 " --> pdb=" O THR E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 281 No H-bonds generated for 'chain 'E' and resid 278 through 281' Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 307 through 309 No H-bonds generated for 'chain 'E' and resid 307 through 309' Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 382 through 401 removed outlier: 3.896A pdb=" N ALA E 400 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 415 through 436 Processing helix chain 'F' and resid 10 through 27 Processing helix chain 'F' and resid 41 through 47 removed outlier: 3.558A pdb=" N GLU F 47 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 73 through 80 Processing helix chain 'F' and resid 84 through 86 No H-bonds generated for 'chain 'F' and resid 84 through 86' Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 103 through 107 Processing helix chain 'F' and resid 110 through 128 removed outlier: 4.633A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.764A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 Processing helix chain 'F' and resid 224 through 243 removed outlier: 3.684A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 288 through 295 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 307 through 309 No H-bonds generated for 'chain 'F' and resid 307 through 309' Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 382 through 401 removed outlier: 4.288A pdb=" N ARG F 400 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 removed outlier: 4.108A pdb=" N GLU F 411 " --> pdb=" O TRP F 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 437 Processing helix chain 'N' and resid 17 through 28 Processing helix chain 'N' and resid 35 through 40 removed outlier: 3.562A pdb=" N SER N 40 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 51 Processing helix chain 'N' and resid 58 through 60 No H-bonds generated for 'chain 'N' and resid 58 through 60' Processing helix chain 'N' and resid 68 through 85 Processing helix chain 'N' and resid 93 through 97 Processing helix chain 'N' and resid 101 through 118 Processing helix chain 'N' and resid 126 through 130 Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 73 through 80 removed outlier: 3.634A pdb=" N VAL J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 103 through 107 Processing helix chain 'J' and resid 111 through 113 No H-bonds generated for 'chain 'J' and resid 111 through 113' Processing helix chain 'J' and resid 115 through 128 removed outlier: 3.621A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 160 removed outlier: 4.083A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 197 removed outlier: 3.559A pdb=" N LEU J 189 " --> pdb=" O ASN J 186 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR J 190 " --> pdb=" O SER J 187 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR J 194 " --> pdb=" O THR J 191 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU J 195 " --> pdb=" O HIS J 192 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU J 196 " --> pdb=" O THR J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 217 Processing helix chain 'J' and resid 224 through 243 removed outlier: 4.478A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 removed outlier: 3.918A pdb=" N GLN J 256 " --> pdb=" O LEU J 252 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR J 257 " --> pdb=" O THR J 253 " (cutoff:3.500A) Processing helix chain 'J' and resid 278 through 281 No H-bonds generated for 'chain 'J' and resid 278 through 281' Processing helix chain 'J' and resid 288 through 296 Processing helix chain 'J' and resid 298 through 300 No H-bonds generated for 'chain 'J' and resid 298 through 300' Processing helix chain 'J' and resid 307 through 309 No H-bonds generated for 'chain 'J' and resid 307 through 309' Processing helix chain 'J' and resid 325 through 337 Processing helix chain 'J' and resid 382 through 401 removed outlier: 3.894A pdb=" N ALA J 400 " --> pdb=" O LEU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 Processing helix chain 'J' and resid 415 through 436 Processing helix chain 'G' and resid 10 through 27 Processing helix chain 'G' and resid 41 through 47 removed outlier: 3.558A pdb=" N GLU G 47 " --> pdb=" O LEU G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 51 No H-bonds generated for 'chain 'G' and resid 49 through 51' Processing helix chain 'G' and resid 73 through 80 Processing helix chain 'G' and resid 84 through 86 No H-bonds generated for 'chain 'G' and resid 84 through 86' Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 103 through 107 Processing helix chain 'G' and resid 110 through 128 removed outlier: 4.633A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.763A pdb=" N GLU G 196 " --> pdb=" O HIS G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 215 Processing helix chain 'G' and resid 224 through 243 removed outlier: 3.684A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N LEU G 242 " --> pdb=" O VAL G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 288 through 295 Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 307 through 309 No H-bonds generated for 'chain 'G' and resid 307 through 309' Processing helix chain 'G' and resid 325 through 338 Processing helix chain 'G' and resid 340 through 342 No H-bonds generated for 'chain 'G' and resid 340 through 342' Processing helix chain 'G' and resid 382 through 401 removed outlier: 4.289A pdb=" N ARG G 400 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 411 removed outlier: 4.110A pdb=" N GLU G 411 " --> pdb=" O TRP G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 437 Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.632A pdb=" N VAL C 78 " --> pdb=" O VAL C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 91 No H-bonds generated for 'chain 'C' and resid 89 through 91' Processing helix chain 'C' and resid 103 through 107 Processing helix chain 'C' and resid 111 through 113 No H-bonds generated for 'chain 'C' and resid 111 through 113' Processing helix chain 'C' and resid 115 through 128 removed outlier: 3.617A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 4.081A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.554A pdb=" N LEU C 189 " --> pdb=" O ASN C 186 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR C 190 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 195 " --> pdb=" O HIS C 192 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU C 196 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.482A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 removed outlier: 3.920A pdb=" N GLN C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR C 257 " --> pdb=" O THR C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 281 No H-bonds generated for 'chain 'C' and resid 278 through 281' Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 307 through 309 No H-bonds generated for 'chain 'C' and resid 307 through 309' Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.897A pdb=" N ALA C 400 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 415 through 436 Processing helix chain 'D' and resid 10 through 27 Processing helix chain 'D' and resid 41 through 47 removed outlier: 3.559A pdb=" N GLU D 47 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 73 through 80 Processing helix chain 'D' and resid 84 through 86 No H-bonds generated for 'chain 'D' and resid 84 through 86' Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 110 through 128 removed outlier: 4.633A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.763A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 224 through 243 removed outlier: 3.683A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 288 through 295 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 307 through 309 No H-bonds generated for 'chain 'D' and resid 307 through 309' Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 382 through 401 removed outlier: 4.288A pdb=" N ARG D 400 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 removed outlier: 4.110A pdb=" N GLU D 411 " --> pdb=" O TRP D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 437 Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 49 through 51 No H-bonds generated for 'chain 'L' and resid 49 through 51' Processing helix chain 'L' and resid 73 through 80 removed outlier: 3.632A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 103 through 107 Processing helix chain 'L' and resid 111 through 113 No H-bonds generated for 'chain 'L' and resid 111 through 113' Processing helix chain 'L' and resid 115 through 128 removed outlier: 3.617A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 160 removed outlier: 4.080A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 197 removed outlier: 3.555A pdb=" N LEU L 189 " --> pdb=" O ASN L 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR L 190 " --> pdb=" O SER L 187 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR L 194 " --> pdb=" O THR L 191 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU L 195 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLU L 196 " --> pdb=" O THR L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 217 Processing helix chain 'L' and resid 224 through 243 removed outlier: 4.481A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 259 removed outlier: 3.918A pdb=" N GLN L 256 " --> pdb=" O LEU L 252 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR L 257 " --> pdb=" O THR L 253 " (cutoff:3.500A) Processing helix chain 'L' and resid 278 through 281 No H-bonds generated for 'chain 'L' and resid 278 through 281' Processing helix chain 'L' and resid 288 through 296 Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 307 through 309 No H-bonds generated for 'chain 'L' and resid 307 through 309' Processing helix chain 'L' and resid 325 through 337 Processing helix chain 'L' and resid 382 through 401 removed outlier: 3.897A pdb=" N ALA L 400 " --> pdb=" O LEU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 Processing helix chain 'L' and resid 415 through 436 Processing helix chain 'I' and resid 10 through 27 Processing helix chain 'I' and resid 41 through 47 removed outlier: 3.558A pdb=" N GLU I 47 " --> pdb=" O LEU I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 51 No H-bonds generated for 'chain 'I' and resid 49 through 51' Processing helix chain 'I' and resid 73 through 80 Processing helix chain 'I' and resid 84 through 86 No H-bonds generated for 'chain 'I' and resid 84 through 86' Processing helix chain 'I' and resid 89 through 91 No H-bonds generated for 'chain 'I' and resid 89 through 91' Processing helix chain 'I' and resid 103 through 107 Processing helix chain 'I' and resid 110 through 128 removed outlier: 4.633A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 160 Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.764A pdb=" N GLU I 196 " --> pdb=" O HIS I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 215 Processing helix chain 'I' and resid 224 through 243 removed outlier: 3.682A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU I 242 " --> pdb=" O VAL I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 288 through 295 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 307 through 309 No H-bonds generated for 'chain 'I' and resid 307 through 309' Processing helix chain 'I' and resid 325 through 338 Processing helix chain 'I' and resid 340 through 342 No H-bonds generated for 'chain 'I' and resid 340 through 342' Processing helix chain 'I' and resid 382 through 401 removed outlier: 4.289A pdb=" N ARG I 400 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 411 removed outlier: 4.110A pdb=" N GLU I 411 " --> pdb=" O TRP I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 437 Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.632A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 91 No H-bonds generated for 'chain 'A' and resid 89 through 91' Processing helix chain 'A' and resid 103 through 107 Processing helix chain 'A' and resid 111 through 113 No H-bonds generated for 'chain 'A' and resid 111 through 113' Processing helix chain 'A' and resid 115 through 128 removed outlier: 3.617A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.082A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.555A pdb=" N LEU A 189 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 190 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 194 " --> pdb=" O THR A 191 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 195 " --> pdb=" O HIS A 192 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLU A 196 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.480A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 removed outlier: 3.920A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.896A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 10 through 27 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.558A pdb=" N GLU B 47 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 73 through 80 Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 107 Processing helix chain 'B' and resid 110 through 128 removed outlier: 4.633A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.763A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 224 through 243 removed outlier: 3.683A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 288 through 295 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 307 through 309 No H-bonds generated for 'chain 'B' and resid 307 through 309' Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 382 through 401 removed outlier: 4.289A pdb=" N ARG B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 4.109A pdb=" N GLU B 411 " --> pdb=" O TRP B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 437 Processing helix chain 'M' and resid 17 through 28 Processing helix chain 'M' and resid 35 through 40 removed outlier: 3.563A pdb=" N SER M 40 " --> pdb=" O GLN M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 51 Processing helix chain 'M' and resid 58 through 60 No H-bonds generated for 'chain 'M' and resid 58 through 60' Processing helix chain 'M' and resid 68 through 85 Processing helix chain 'M' and resid 93 through 97 Processing helix chain 'M' and resid 101 through 118 Processing helix chain 'M' and resid 126 through 130 Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 49 through 51 No H-bonds generated for 'chain 'K' and resid 49 through 51' Processing helix chain 'K' and resid 73 through 80 removed outlier: 3.632A pdb=" N VAL K 78 " --> pdb=" O VAL K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 91 No H-bonds generated for 'chain 'K' and resid 89 through 91' Processing helix chain 'K' and resid 103 through 107 Processing helix chain 'K' and resid 111 through 113 No H-bonds generated for 'chain 'K' and resid 111 through 113' Processing helix chain 'K' and resid 115 through 128 removed outlier: 3.617A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 160 removed outlier: 4.080A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 197 removed outlier: 3.556A pdb=" N LEU K 189 " --> pdb=" O ASN K 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR K 190 " --> pdb=" O SER K 187 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR K 194 " --> pdb=" O THR K 191 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU K 195 " --> pdb=" O HIS K 192 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N GLU K 196 " --> pdb=" O THR K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 217 Processing helix chain 'K' and resid 224 through 243 removed outlier: 4.481A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 removed outlier: 3.918A pdb=" N GLN K 256 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR K 257 " --> pdb=" O THR K 253 " (cutoff:3.500A) Processing helix chain 'K' and resid 278 through 281 No H-bonds generated for 'chain 'K' and resid 278 through 281' Processing helix chain 'K' and resid 288 through 296 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 307 through 309 No H-bonds generated for 'chain 'K' and resid 307 through 309' Processing helix chain 'K' and resid 325 through 337 Processing helix chain 'K' and resid 382 through 401 removed outlier: 3.896A pdb=" N ALA K 400 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 410 Processing helix chain 'K' and resid 415 through 436 Processing helix chain 'H' and resid 10 through 27 Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.558A pdb=" N GLU H 47 " --> pdb=" O LEU H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 73 through 80 Processing helix chain 'H' and resid 84 through 86 No H-bonds generated for 'chain 'H' and resid 84 through 86' Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 103 through 107 Processing helix chain 'H' and resid 110 through 128 removed outlier: 4.634A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.764A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 215 Processing helix chain 'H' and resid 224 through 243 removed outlier: 3.684A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 259 Processing helix chain 'H' and resid 288 through 295 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 307 through 309 No H-bonds generated for 'chain 'H' and resid 307 through 309' Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 340 through 342 No H-bonds generated for 'chain 'H' and resid 340 through 342' Processing helix chain 'H' and resid 382 through 401 removed outlier: 4.289A pdb=" N ARG H 400 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 411 removed outlier: 4.110A pdb=" N GLU H 411 " --> pdb=" O TRP H 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 437 Processing sheet with id= A, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.027A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY E 134 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE E 7 " --> pdb=" O GLY E 134 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU E 136 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL E 9 " --> pdb=" O LEU E 136 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE E 138 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'E' and resid 268 through 273 removed outlier: 3.596A pdb=" N ALA E 314 " --> pdb=" O ASN E 380 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL F 5 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE F 7 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ALA F 9 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS F 139 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU F 137 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN F 167 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N HIS F 139 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU F 200 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER F 170 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N VAL F 172 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE F 204 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ASP F 205 " --> pdb=" O PRO F 270 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N PHE F 272 " --> pdb=" O ASP F 205 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE F 267 " --> pdb=" O SER F 381 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER F 381 " --> pdb=" O PHE F 267 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.814A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.028A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLY J 134 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE J 7 " --> pdb=" O GLY J 134 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU J 136 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N VAL J 9 " --> pdb=" O LEU J 136 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE J 138 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL J 137 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU J 167 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N HIS J 139 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE J 169 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER J 170 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N PHE J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N TYR J 172 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL J 204 " --> pdb=" O TYR J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= H, first strand: chain 'J' and resid 268 through 273 removed outlier: 3.591A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.887A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL G 5 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ILE G 7 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA G 9 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N HIS G 139 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE G 165 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU G 137 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN G 167 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N HIS G 139 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE G 169 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU G 200 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER G 170 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL G 172 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE G 204 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASP G 205 " --> pdb=" O PRO G 270 " (cutoff:3.500A) removed outlier: 11.774A pdb=" N PHE G 272 " --> pdb=" O ASP G 205 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N PHE G 267 " --> pdb=" O SER G 381 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER G 381 " --> pdb=" O PHE G 267 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.814A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.027A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY C 134 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE C 7 " --> pdb=" O GLY C 134 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU C 136 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL C 9 " --> pdb=" O LEU C 136 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE C 138 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= M, first strand: chain 'C' and resid 268 through 273 removed outlier: 3.595A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL D 5 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE D 7 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA D 9 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS D 139 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU D 137 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ASN D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N HIS D 139 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N PHE D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU D 200 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER D 170 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N TYR D 202 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL D 172 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE D 204 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASP D 205 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 11.776A pdb=" N PHE D 272 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N PHE D 267 " --> pdb=" O SER D 381 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER D 381 " --> pdb=" O PHE D 267 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.814A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.028A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY L 134 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE L 7 " --> pdb=" O GLY L 134 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU L 136 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL L 9 " --> pdb=" O LEU L 136 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE L 138 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N SER L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL L 137 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU L 167 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS L 139 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE L 169 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER L 170 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N PHE L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR L 172 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL L 204 " --> pdb=" O TYR L 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'L' and resid 53 through 55 Processing sheet with id= R, first strand: chain 'L' and resid 268 through 273 removed outlier: 3.594A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N VAL I 5 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE I 7 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA I 9 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS I 139 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE I 165 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU I 137 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN I 167 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 8.219A pdb=" N HIS I 139 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU I 200 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER I 170 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL I 172 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE I 204 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ASP I 205 " --> pdb=" O PRO I 270 " (cutoff:3.500A) removed outlier: 11.771A pdb=" N PHE I 272 " --> pdb=" O ASP I 205 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE I 267 " --> pdb=" O SER I 381 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N SER I 381 " --> pdb=" O PHE I 267 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.813A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.027A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLY A 134 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE A 7 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU A 136 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL A 9 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE A 138 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= W, first strand: chain 'A' and resid 268 through 273 removed outlier: 3.595A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL B 172 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE B 204 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ASP B 205 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 11.777A pdb=" N PHE B 272 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N PHE B 267 " --> pdb=" O SER B 381 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N SER B 381 " --> pdb=" O PHE B 267 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.813A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.027A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY K 134 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE K 7 " --> pdb=" O GLY K 134 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU K 136 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N VAL K 9 " --> pdb=" O LEU K 136 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE K 138 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AB, first strand: chain 'K' and resid 268 through 273 removed outlier: 3.593A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.888A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE H 7 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ALA H 9 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU H 137 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN H 167 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N HIS H 139 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLU H 200 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N SER H 170 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N TYR H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL H 172 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE H 204 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N ASP H 205 " --> pdb=" O PRO H 270 " (cutoff:3.500A) removed outlier: 11.773A pdb=" N PHE H 272 " --> pdb=" O ASP H 205 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N PHE H 267 " --> pdb=" O SER H 381 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N SER H 381 " --> pdb=" O PHE H 267 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.813A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) 1880 hydrogen bonds defined for protein. 4890 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: 17.21 Time building geometry restraints manager: 18.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7302 1.32 - 1.44: 11914 1.44 - 1.57: 24261 1.57 - 1.69: 55 1.69 - 1.81: 466 Bond restraints: 43998 Sorted by residual: bond pdb=" O3B G2P D 501 " pdb=" PB G2P D 501 " ideal model delta sigma weight residual 1.612 1.477 0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" O3B G2P I 501 " pdb=" PB G2P I 501 " ideal model delta sigma weight residual 1.612 1.478 0.134 2.00e-02 2.50e+03 4.51e+01 bond pdb=" O3B G2P B 501 " pdb=" PB G2P B 501 " ideal model delta sigma weight residual 1.612 1.478 0.134 2.00e-02 2.50e+03 4.50e+01 bond pdb=" O3B G2P H 501 " pdb=" PB G2P H 501 " ideal model delta sigma weight residual 1.612 1.479 0.133 2.00e-02 2.50e+03 4.43e+01 bond pdb=" O3B G2P F 501 " pdb=" PB G2P F 501 " ideal model delta sigma weight residual 1.612 1.479 0.133 2.00e-02 2.50e+03 4.41e+01 ... (remaining 43993 not shown) Histogram of bond angle deviations from ideal: 92.39 - 101.38: 149 101.38 - 110.36: 10555 110.36 - 119.35: 26435 119.35 - 128.33: 22232 128.33 - 137.32: 375 Bond angle restraints: 59746 Sorted by residual: angle pdb=" O VAL G 288 " pdb=" C VAL G 288 " pdb=" N PRO G 289 " ideal model delta sigma weight residual 120.07 124.01 -3.94 7.10e-01 1.98e+00 3.07e+01 angle pdb=" O VAL H 288 " pdb=" C VAL H 288 " pdb=" N PRO H 289 " ideal model delta sigma weight residual 120.07 124.00 -3.93 7.10e-01 1.98e+00 3.06e+01 angle pdb=" O VAL D 288 " pdb=" C VAL D 288 " pdb=" N PRO D 289 " ideal model delta sigma weight residual 120.07 123.97 -3.90 7.10e-01 1.98e+00 3.01e+01 angle pdb=" O VAL F 288 " pdb=" C VAL F 288 " pdb=" N PRO F 289 " ideal model delta sigma weight residual 120.07 123.97 -3.90 7.10e-01 1.98e+00 3.01e+01 angle pdb=" O VAL B 288 " pdb=" C VAL B 288 " pdb=" N PRO B 289 " ideal model delta sigma weight residual 120.07 123.97 -3.90 7.10e-01 1.98e+00 3.01e+01 ... (remaining 59741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 25455 33.88 - 67.76: 749 67.76 - 101.64: 35 101.64 - 135.52: 1 135.52 - 169.40: 18 Dihedral angle restraints: 26258 sinusoidal: 10554 harmonic: 15704 Sorted by residual: dihedral pdb=" C5' GTP J 501 " pdb=" O5' GTP J 501 " pdb=" PA GTP J 501 " pdb=" O3A GTP J 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.33 -169.40 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP K 501 " pdb=" O5' GTP K 501 " pdb=" PA GTP K 501 " pdb=" O3A GTP K 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.56 -169.17 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' GTP L 501 " pdb=" O5' GTP L 501 " pdb=" PA GTP L 501 " pdb=" O3A GTP L 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.58 -169.15 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 26255 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4997 0.094 - 0.188: 1283 0.188 - 0.283: 205 0.283 - 0.377: 31 0.377 - 0.471: 6 Chirality restraints: 6522 Sorted by residual: chirality pdb=" C3' G2P I 501 " pdb=" C2' G2P I 501 " pdb=" C4' G2P I 501 " pdb=" O3' G2P I 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.24 -0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" C3' G2P D 501 " pdb=" C2' G2P D 501 " pdb=" C4' G2P D 501 " pdb=" O3' G2P D 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.24 -0.47 2.00e-01 2.50e+01 5.53e+00 chirality pdb=" C3' G2P F 501 " pdb=" C2' G2P F 501 " pdb=" C4' G2P F 501 " pdb=" O3' G2P F 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.24 -0.47 2.00e-01 2.50e+01 5.46e+00 ... (remaining 6519 not shown) Planarity restraints: 7776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA N 117 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ALA N 117 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA N 117 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN N 118 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS C 88 " -0.037 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO C 89 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 89 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 89 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS L 88 " -0.037 5.00e-02 4.00e+02 5.69e-02 5.19e+00 pdb=" N PRO L 89 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO L 89 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 89 " -0.032 5.00e-02 4.00e+02 ... (remaining 7773 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 58 2.54 - 3.13: 32069 3.13 - 3.72: 67400 3.72 - 4.31: 97655 4.31 - 4.90: 165058 Nonbonded interactions: 362240 Sorted by model distance: nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 1.948 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.953 2.170 nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 1.959 2.170 nonbonded pdb=" O1B GTP C 501 " pdb="MG MG C 502 " model vdw 1.962 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 1.978 2.170 ... (remaining 362235 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.080 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: 0.030 Extract box with map and model: 28.900 Check model and map are aligned: 0.650 Set scattering table: 0.400 Process input model: 110.610 Find NCS groups from input model: 3.260 Set up NCS constraints: 0.430 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 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 : 0.009 0.135 43998 Z= 0.599 Angle : 1.457 15.082 59746 Z= 0.985 Chirality : 0.084 0.471 6522 Planarity : 0.006 0.057 7776 Dihedral : 15.874 169.404 16178 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.86 % Favored : 97.03 % Rotamer: Outliers : 1.21 % Allowed : 6.65 % Favored : 92.14 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 4.88 % 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: 0.16 (0.11), residues: 5388 helix: 0.95 (0.09), residues: 2420 sheet: 0.36 (0.19), residues: 774 loop : -0.89 (0.12), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 21 HIS 0.012 0.002 HIS C 8 PHE 0.024 0.002 PHE C 351 TYR 0.019 0.003 TYR I 61 ARG 0.022 0.001 ARG F 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 968 time to evaluate : 4.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.8416 (mmm) cc_final: 0.7759 (mmp) REVERT: E 302 MET cc_start: 0.7604 (mtt) cc_final: 0.7363 (mtt) REVERT: E 398 MET cc_start: 0.8428 (mtp) cc_final: 0.8147 (mtm) REVERT: F 278 ARG cc_start: 0.8798 (mmm-85) cc_final: 0.8564 (mtm-85) REVERT: F 314 THR cc_start: 0.8795 (p) cc_final: 0.8582 (p) REVERT: N 28 LEU cc_start: 0.8351 (mp) cc_final: 0.8032 (mp) REVERT: N 38 LEU cc_start: 0.8347 (mp) cc_final: 0.8000 (mp) REVERT: N 100 LYS cc_start: 0.5114 (mmtp) cc_final: 0.4638 (ptmt) REVERT: J 154 MET cc_start: 0.8155 (mmm) cc_final: 0.7626 (mmt) REVERT: J 302 MET cc_start: 0.7224 (mtt) cc_final: 0.7017 (mtt) REVERT: J 398 MET cc_start: 0.8666 (mtp) cc_final: 0.8414 (mtm) REVERT: G 59 ASN cc_start: 0.8388 (m110) cc_final: 0.7941 (p0) REVERT: G 97 SER cc_start: 0.8634 (m) cc_final: 0.8382 (p) REVERT: G 314 THR cc_start: 0.8956 (p) cc_final: 0.8516 (p) REVERT: C 253 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8338 (m) REVERT: C 285 GLN cc_start: 0.8320 (pt0) cc_final: 0.7792 (mm110) REVERT: D 166 MET cc_start: 0.8088 (tpp) cc_final: 0.7834 (tpt) REVERT: D 334 ASN cc_start: 0.8326 (t0) cc_final: 0.8093 (t0) REVERT: L 127 ASP cc_start: 0.8408 (m-30) cc_final: 0.8192 (m-30) REVERT: L 154 MET cc_start: 0.8328 (mmm) cc_final: 0.8081 (tpp) REVERT: L 253 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8807 (t) REVERT: I 59 ASN cc_start: 0.8247 (m110) cc_final: 0.7877 (p0) REVERT: I 129 CYS cc_start: 0.7298 (m) cc_final: 0.6913 (m) REVERT: A 154 MET cc_start: 0.8565 (mmm) cc_final: 0.8319 (mmt) REVERT: A 439 SER cc_start: 0.7930 (m) cc_final: 0.7413 (p) REVERT: M 20 MET cc_start: 0.7266 (ttp) cc_final: 0.6472 (mtt) REVERT: M 28 LEU cc_start: 0.8098 (mp) cc_final: 0.7694 (mp) REVERT: M 32 TYR cc_start: 0.6879 (m-10) cc_final: 0.6626 (m-80) REVERT: M 37 GLN cc_start: 0.7197 (mt0) cc_final: 0.6788 (mt0) REVERT: M 100 LYS cc_start: 0.5788 (mmtp) cc_final: 0.5071 (ptmt) REVERT: K 253 THR cc_start: 0.8865 (OUTLIER) cc_final: 0.8591 (t) REVERT: K 431 ASP cc_start: 0.7602 (m-30) cc_final: 0.7320 (m-30) REVERT: H 59 ASN cc_start: 0.8459 (m110) cc_final: 0.8145 (p0) REVERT: H 75 MET cc_start: 0.8779 (mmt) cc_final: 0.8457 (mmt) REVERT: H 161 TYR cc_start: 0.8599 (m-80) cc_final: 0.8322 (m-80) REVERT: H 373 MET cc_start: 0.7990 (ptp) cc_final: 0.7779 (ptm) outliers start: 56 outliers final: 21 residues processed: 1016 average time/residue: 0.5941 time to fit residues: 955.3767 Evaluate side-chains 552 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 528 time to evaluate : 4.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 253 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 452 optimal weight: 0.8980 chunk 406 optimal weight: 0.7980 chunk 225 optimal weight: 3.9990 chunk 138 optimal weight: 0.5980 chunk 274 optimal weight: 5.9990 chunk 217 optimal weight: 4.9990 chunk 420 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 chunk 312 optimal weight: 0.9980 chunk 486 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 HIS E 186 ASN E 256 GLN ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 HIS F 101 ASN ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 ASN F 349 ASN F 406 HIS N 104 ASN ** J 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 101 ASN G 133 GLN G 228 ASN G 309 HIS C 186 ASN C 283 HIS C 293 ASN C 309 HIS ** D 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 139 HIS D 228 ASN D 247 GLN D 281 GLN L 18 ASN ** L 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 ASN L 283 HIS I 139 HIS I 228 ASN I 229 HIS I 309 HIS A 186 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 HIS ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 HIS B 228 ASN B 281 GLN B 349 ASN B 406 HIS M 104 ASN K 18 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 186 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 133 GLN H 139 HIS H 228 ASN H 229 HIS H 309 HIS Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 43998 Z= 0.183 Angle : 0.563 7.769 59746 Z= 0.300 Chirality : 0.042 0.165 6522 Planarity : 0.005 0.050 7776 Dihedral : 11.587 177.472 6168 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.10 % Allowed : 11.41 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 1.14 (0.11), residues: 5388 helix: 2.07 (0.11), residues: 2402 sheet: 0.61 (0.17), residues: 798 loop : -0.68 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 346 HIS 0.005 0.001 HIS H 139 PHE 0.016 0.001 PHE M 114 TYR 0.017 0.001 TYR J 24 ARG 0.007 0.001 ARG J 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 588 time to evaluate : 4.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 ASP cc_start: 0.8179 (m-30) cc_final: 0.7957 (m-30) REVERT: E 154 MET cc_start: 0.8652 (mmm) cc_final: 0.8078 (mmt) REVERT: E 302 MET cc_start: 0.7713 (mtt) cc_final: 0.7447 (mtt) REVERT: E 398 MET cc_start: 0.8436 (mtp) cc_final: 0.8208 (mtm) REVERT: F 269 MET cc_start: 0.7834 (mtp) cc_final: 0.7589 (mtm) REVERT: F 314 THR cc_start: 0.8581 (p) cc_final: 0.8319 (p) REVERT: N 32 TYR cc_start: 0.6805 (m-10) cc_final: 0.6256 (m-80) REVERT: N 50 MET cc_start: 0.5765 (ttp) cc_final: 0.5490 (ttm) REVERT: N 100 LYS cc_start: 0.4946 (mmtp) cc_final: 0.4220 (ptmt) REVERT: N 107 PHE cc_start: 0.8220 (t80) cc_final: 0.7875 (t80) REVERT: J 186 ASN cc_start: 0.8659 (m-40) cc_final: 0.8425 (m-40) REVERT: J 297 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7863 (tm-30) REVERT: J 398 MET cc_start: 0.8674 (mtp) cc_final: 0.8329 (mtm) REVERT: G 47 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8022 (mm-30) REVERT: G 59 ASN cc_start: 0.8553 (m110) cc_final: 0.7986 (p0) REVERT: G 75 MET cc_start: 0.8902 (mmt) cc_final: 0.8304 (mmt) REVERT: C 285 GLN cc_start: 0.8275 (pt0) cc_final: 0.7692 (mm110) REVERT: C 306 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7565 (p0) REVERT: D 299 LYS cc_start: 0.8416 (ptmt) cc_final: 0.8095 (tttp) REVERT: L 224 TYR cc_start: 0.8720 (OUTLIER) cc_final: 0.8447 (m-10) REVERT: L 256 GLN cc_start: 0.8499 (pt0) cc_final: 0.7999 (tm-30) REVERT: L 284 GLU cc_start: 0.8305 (pt0) cc_final: 0.8004 (pm20) REVERT: I 59 ASN cc_start: 0.8401 (m110) cc_final: 0.7978 (p0) REVERT: I 129 CYS cc_start: 0.7280 (m) cc_final: 0.6980 (m) REVERT: A 154 MET cc_start: 0.8633 (mmm) cc_final: 0.8358 (mmt) REVERT: B 299 LYS cc_start: 0.8585 (ptmt) cc_final: 0.8207 (tmtt) REVERT: M 20 MET cc_start: 0.7304 (ttp) cc_final: 0.6630 (mtt) REVERT: M 32 TYR cc_start: 0.7105 (m-10) cc_final: 0.6708 (m-80) REVERT: M 50 MET cc_start: 0.6079 (OUTLIER) cc_final: 0.5834 (ppp) REVERT: M 100 LYS cc_start: 0.5794 (mmtp) cc_final: 0.5011 (ptmt) REVERT: K 186 ASN cc_start: 0.8638 (m-40) cc_final: 0.8379 (m-40) REVERT: K 253 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8529 (m) REVERT: K 413 MET cc_start: 0.7804 (ttm) cc_final: 0.7474 (ttm) REVERT: K 425 MET cc_start: 0.8232 (tpp) cc_final: 0.7954 (tpp) REVERT: K 431 ASP cc_start: 0.7589 (m-30) cc_final: 0.7342 (m-30) REVERT: H 47 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7904 (mm-30) REVERT: H 59 ASN cc_start: 0.8497 (m110) cc_final: 0.8196 (p0) REVERT: H 349 ASN cc_start: 0.7833 (m-40) cc_final: 0.7559 (t0) outliers start: 97 outliers final: 44 residues processed: 664 average time/residue: 0.5308 time to fit residues: 585.5191 Evaluate side-chains 528 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 480 time to evaluate : 4.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 315 CYS Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 224 TYR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 113 GLU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 156 LYS Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 253 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 213 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 270 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 405 optimal weight: 3.9990 chunk 331 optimal weight: 5.9990 chunk 134 optimal weight: 10.0000 chunk 487 optimal weight: 9.9990 chunk 526 optimal weight: 5.9990 chunk 434 optimal weight: 1.9990 chunk 483 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 391 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 8 HIS E 88 HIS ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 HIS F 258 ASN F 293 GLN F 309 HIS F 433 GLN N 104 ASN J 8 HIS J 216 ASN J 283 HIS J 293 ASN G 101 ASN G 139 HIS G 229 HIS G 433 GLN C 8 HIS C 28 HIS D 14 ASN D 258 ASN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS D 433 GLN L 8 HIS L 28 HIS I 133 GLN I 433 GLN A 8 HIS A 28 HIS A 88 HIS A 256 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN B 247 GLN B 258 ASN B 309 HIS ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 ASN K 8 HIS K 28 HIS ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 433 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 43998 Z= 0.336 Angle : 0.574 11.623 59746 Z= 0.300 Chirality : 0.044 0.161 6522 Planarity : 0.005 0.051 7776 Dihedral : 11.317 177.817 6157 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.99 % Allowed : 12.91 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.80 (0.11), residues: 5388 helix: 1.74 (0.11), residues: 2432 sheet: 0.41 (0.18), residues: 780 loop : -0.80 (0.13), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 21 HIS 0.009 0.001 HIS E 88 PHE 0.018 0.002 PHE N 115 TYR 0.031 0.002 TYR L 24 ARG 0.006 0.001 ARG I 278 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 468 time to evaluate : 4.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 ASP cc_start: 0.8235 (m-30) cc_final: 0.7999 (m-30) REVERT: E 154 MET cc_start: 0.8571 (mmm) cc_final: 0.8268 (mmt) REVERT: E 302 MET cc_start: 0.7798 (mtt) cc_final: 0.7487 (mtt) REVERT: F 269 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7645 (mtp) REVERT: N 32 TYR cc_start: 0.7084 (m-10) cc_final: 0.6823 (m-80) REVERT: N 100 LYS cc_start: 0.5042 (mmtp) cc_final: 0.4307 (ptmt) REVERT: J 186 ASN cc_start: 0.8741 (m-40) cc_final: 0.8521 (m-40) REVERT: J 297 GLU cc_start: 0.8299 (tm-30) cc_final: 0.7875 (tm-30) REVERT: J 309 HIS cc_start: 0.8221 (m90) cc_final: 0.7754 (m90) REVERT: J 398 MET cc_start: 0.8644 (mtp) cc_final: 0.8312 (mtm) REVERT: G 47 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8083 (mm-30) REVERT: G 323 MET cc_start: 0.8422 (ptp) cc_final: 0.8112 (ptp) REVERT: C 120 ASP cc_start: 0.7999 (m-30) cc_final: 0.7773 (m-30) REVERT: D 299 LYS cc_start: 0.8664 (ptmt) cc_final: 0.8341 (tttp) REVERT: L 127 ASP cc_start: 0.8486 (m-30) cc_final: 0.8200 (m-30) REVERT: L 256 GLN cc_start: 0.8579 (pt0) cc_final: 0.8068 (tm-30) REVERT: L 284 GLU cc_start: 0.8422 (pt0) cc_final: 0.8118 (pm20) REVERT: L 309 HIS cc_start: 0.8313 (m90) cc_final: 0.8110 (m90) REVERT: I 129 CYS cc_start: 0.7200 (m) cc_final: 0.6955 (m) REVERT: M 32 TYR cc_start: 0.7168 (m-10) cc_final: 0.6474 (m-80) REVERT: M 34 LYS cc_start: 0.7375 (mmmt) cc_final: 0.6747 (mppt) REVERT: M 37 GLN cc_start: 0.7552 (mp10) cc_final: 0.7235 (mp10) REVERT: M 95 LYS cc_start: 0.7724 (mttm) cc_final: 0.7247 (mmtt) REVERT: M 100 LYS cc_start: 0.5671 (mmtp) cc_final: 0.4815 (ptmt) REVERT: K 186 ASN cc_start: 0.8695 (m-40) cc_final: 0.8458 (m-40) REVERT: K 309 HIS cc_start: 0.8087 (m90) cc_final: 0.7668 (m90) REVERT: K 425 MET cc_start: 0.8508 (tpp) cc_final: 0.8297 (tpp) REVERT: H 26 ASP cc_start: 0.7954 (t0) cc_final: 0.7558 (t0) REVERT: H 41 ASP cc_start: 0.7042 (p0) cc_final: 0.6681 (p0) REVERT: H 47 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8061 (mm-30) REVERT: H 349 ASN cc_start: 0.8125 (m-40) cc_final: 0.7859 (t0) REVERT: H 435 TYR cc_start: 0.9110 (m-80) cc_final: 0.8707 (m-10) outliers start: 138 outliers final: 81 residues processed: 573 average time/residue: 0.5280 time to fit residues: 503.3414 Evaluate side-chains 505 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 423 time to evaluate : 4.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 115 ILE Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 269 MET Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 113 GLU Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 221 THR Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 101 ASN Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 213 CYS Chi-restraints excluded: chain I residue 221 THR Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 221 THR Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 481 optimal weight: 5.9990 chunk 366 optimal weight: 10.0000 chunk 253 optimal weight: 3.9990 chunk 53 optimal weight: 0.0570 chunk 232 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 489 optimal weight: 0.9990 chunk 518 optimal weight: 6.9990 chunk 255 optimal weight: 1.9990 chunk 463 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 overall best weight: 1.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 28 HIS E 88 HIS ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 229 HIS F 281 GLN F 436 GLN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 293 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 43998 Z= 0.186 Angle : 0.507 13.087 59746 Z= 0.262 Chirality : 0.041 0.151 6522 Planarity : 0.004 0.046 7776 Dihedral : 11.139 178.341 6155 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.71 % Allowed : 13.32 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.85 (0.11), residues: 5388 helix: 1.69 (0.11), residues: 2462 sheet: 0.40 (0.17), residues: 798 loop : -0.68 (0.13), residues: 2128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 346 HIS 0.009 0.001 HIS E 88 PHE 0.013 0.001 PHE M 114 TYR 0.023 0.001 TYR L 24 ARG 0.005 0.000 ARG B 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 479 time to evaluate : 4.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 88 HIS cc_start: 0.8839 (OUTLIER) cc_final: 0.7115 (t70) REVERT: E 120 ASP cc_start: 0.8213 (m-30) cc_final: 0.7940 (m-30) REVERT: E 302 MET cc_start: 0.7778 (mtt) cc_final: 0.7506 (mtt) REVERT: F 26 ASP cc_start: 0.7836 (t0) cc_final: 0.7558 (t0) REVERT: F 254 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.8406 (mtmt) REVERT: N 100 LYS cc_start: 0.5031 (mmtp) cc_final: 0.4330 (ptmt) REVERT: J 186 ASN cc_start: 0.8806 (m-40) cc_final: 0.8580 (m-40) REVERT: J 297 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7841 (tm-30) REVERT: G 47 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8064 (mm-30) REVERT: G 75 MET cc_start: 0.8906 (mmt) cc_final: 0.8288 (mmt) REVERT: G 323 MET cc_start: 0.8488 (ptp) cc_final: 0.8255 (ptp) REVERT: C 120 ASP cc_start: 0.7973 (m-30) cc_final: 0.7745 (m-30) REVERT: D 299 LYS cc_start: 0.8402 (ptmt) cc_final: 0.8038 (tttp) REVERT: L 127 ASP cc_start: 0.8430 (m-30) cc_final: 0.8110 (m-30) REVERT: L 230 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8409 (mp) REVERT: L 256 GLN cc_start: 0.8561 (pt0) cc_final: 0.8024 (tm-30) REVERT: L 284 GLU cc_start: 0.8359 (pt0) cc_final: 0.8035 (pm20) REVERT: I 59 ASN cc_start: 0.8366 (m-40) cc_final: 0.7979 (p0) REVERT: A 127 ASP cc_start: 0.8679 (m-30) cc_final: 0.8367 (m-30) REVERT: B 278 ARG cc_start: 0.8879 (mmm160) cc_final: 0.8669 (mmm160) REVERT: B 286 LEU cc_start: 0.8544 (tp) cc_final: 0.8335 (pp) REVERT: B 299 LYS cc_start: 0.8749 (ptmt) cc_final: 0.8413 (ttpt) REVERT: M 32 TYR cc_start: 0.7196 (m-10) cc_final: 0.6646 (m-80) REVERT: M 34 LYS cc_start: 0.7386 (mmmt) cc_final: 0.6970 (mptt) REVERT: M 48 MET cc_start: 0.6100 (ttp) cc_final: 0.5537 (tmm) REVERT: M 95 LYS cc_start: 0.7719 (mttm) cc_final: 0.7202 (mmpt) REVERT: M 100 LYS cc_start: 0.5623 (mmtp) cc_final: 0.4800 (ptmt) REVERT: K 172 TYR cc_start: 0.8672 (t80) cc_final: 0.8452 (t80) REVERT: K 186 ASN cc_start: 0.8634 (m-40) cc_final: 0.8387 (m-40) REVERT: H 26 ASP cc_start: 0.7984 (t0) cc_final: 0.7544 (t0) REVERT: H 47 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7911 (mm-30) REVERT: H 286 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7752 (pp) REVERT: H 299 LYS cc_start: 0.8708 (ptmt) cc_final: 0.8332 (tttp) REVERT: H 349 ASN cc_start: 0.8222 (m-40) cc_final: 0.7867 (t0) REVERT: H 435 TYR cc_start: 0.8989 (m-80) cc_final: 0.8632 (m-10) outliers start: 125 outliers final: 76 residues processed: 578 average time/residue: 0.5666 time to fit residues: 554.3789 Evaluate side-chains 507 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 427 time to evaluate : 4.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 163 LYS Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 305 CYS Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 431 optimal weight: 4.9990 chunk 294 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 385 optimal weight: 8.9990 chunk 213 optimal weight: 7.9990 chunk 442 optimal weight: 9.9990 chunk 358 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 264 optimal weight: 0.8980 chunk 465 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 ASN D 309 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 107 HIS ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 43998 Z= 0.330 Angle : 0.550 12.168 59746 Z= 0.283 Chirality : 0.043 0.161 6522 Planarity : 0.004 0.049 7776 Dihedral : 11.153 179.616 6151 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.23 % Allowed : 13.90 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.70 (0.11), residues: 5388 helix: 1.58 (0.11), residues: 2450 sheet: 0.28 (0.18), residues: 780 loop : -0.75 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 346 HIS 0.024 0.001 HIS E 88 PHE 0.017 0.002 PHE F 20 TYR 0.024 0.001 TYR K 24 ARG 0.007 0.001 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 439 time to evaluate : 4.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 ASP cc_start: 0.8186 (m-30) cc_final: 0.7956 (m-30) REVERT: E 302 MET cc_start: 0.7829 (mtt) cc_final: 0.7599 (mtt) REVERT: F 26 ASP cc_start: 0.7937 (t0) cc_final: 0.7661 (t0) REVERT: F 254 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8443 (mtmt) REVERT: N 32 TYR cc_start: 0.7452 (m-10) cc_final: 0.7225 (m-80) REVERT: N 95 LYS cc_start: 0.7734 (mttm) cc_final: 0.6951 (mtmt) REVERT: N 100 LYS cc_start: 0.4987 (mmtp) cc_final: 0.4293 (ptmt) REVERT: J 168 GLU cc_start: 0.7373 (mp0) cc_final: 0.7029 (mt-10) REVERT: J 186 ASN cc_start: 0.8830 (m-40) cc_final: 0.8619 (m-40) REVERT: J 297 GLU cc_start: 0.8294 (tm-30) cc_final: 0.8007 (tm-30) REVERT: G 47 GLU cc_start: 0.8454 (mm-30) cc_final: 0.8220 (mm-30) REVERT: G 75 MET cc_start: 0.8967 (mmt) cc_final: 0.8321 (mmt) REVERT: G 254 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.8227 (mtmt) REVERT: G 323 MET cc_start: 0.8466 (ptp) cc_final: 0.8237 (ptp) REVERT: C 120 ASP cc_start: 0.8047 (m-30) cc_final: 0.7776 (m-30) REVERT: L 127 ASP cc_start: 0.8442 (m-30) cc_final: 0.8230 (m-30) REVERT: L 230 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8479 (mp) REVERT: L 256 GLN cc_start: 0.8613 (pt0) cc_final: 0.8081 (tm-30) REVERT: L 284 GLU cc_start: 0.8368 (pt0) cc_final: 0.7993 (pm20) REVERT: L 327 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: I 59 ASN cc_start: 0.8492 (m-40) cc_final: 0.8067 (p0) REVERT: I 254 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8437 (ttmt) REVERT: A 127 ASP cc_start: 0.8735 (m-30) cc_final: 0.8388 (m-30) REVERT: A 154 MET cc_start: 0.8509 (mmm) cc_final: 0.8186 (mmm) REVERT: B 286 LEU cc_start: 0.8640 (tp) cc_final: 0.8381 (pp) REVERT: M 32 TYR cc_start: 0.7219 (m-10) cc_final: 0.6723 (m-80) REVERT: M 34 LYS cc_start: 0.7426 (mmmt) cc_final: 0.7067 (mppt) REVERT: M 48 MET cc_start: 0.6062 (ttp) cc_final: 0.5591 (tmm) REVERT: M 50 MET cc_start: 0.4217 (ppp) cc_final: 0.4001 (ppp) REVERT: M 95 LYS cc_start: 0.7774 (mttm) cc_final: 0.6931 (mtmt) REVERT: M 100 LYS cc_start: 0.5854 (mmtp) cc_final: 0.4927 (ptmt) REVERT: M 118 ASN cc_start: 0.4137 (m-40) cc_final: 0.3926 (m-40) REVERT: K 18 ASN cc_start: 0.7999 (OUTLIER) cc_final: 0.7744 (m110) REVERT: H 26 ASP cc_start: 0.8069 (t0) cc_final: 0.7661 (t0) REVERT: H 41 ASP cc_start: 0.7218 (p0) cc_final: 0.6829 (p0) REVERT: H 47 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7945 (mm-30) REVERT: H 299 LYS cc_start: 0.8742 (ptmt) cc_final: 0.8413 (tttp) REVERT: H 349 ASN cc_start: 0.8208 (m-40) cc_final: 0.7934 (t0) REVERT: H 435 TYR cc_start: 0.9001 (m-80) cc_final: 0.8616 (m-10) outliers start: 149 outliers final: 100 residues processed: 553 average time/residue: 0.5342 time to fit residues: 490.4258 Evaluate side-chains 520 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 414 time to evaluate : 4.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 54 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 241 CYS Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 163 LYS Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 116 ASP Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 4 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 190 SER Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 116 ASP Chi-restraints excluded: chain I residue 213 CYS Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 213 CYS Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 174 optimal weight: 0.9980 chunk 466 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 304 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 518 optimal weight: 4.9990 chunk 430 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 171 optimal weight: 0.8980 chunk 272 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 HIS D 229 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 301 GLN ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 107 HIS ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 283 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43998 Z= 0.208 Angle : 0.508 11.454 59746 Z= 0.258 Chirality : 0.041 0.234 6522 Planarity : 0.004 0.050 7776 Dihedral : 11.033 179.460 6150 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.51 % Allowed : 14.90 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.80 (0.11), residues: 5388 helix: 1.62 (0.11), residues: 2456 sheet: 0.41 (0.18), residues: 750 loop : -0.66 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 346 HIS 0.011 0.001 HIS E 88 PHE 0.012 0.001 PHE I 377 TYR 0.023 0.001 TYR K 24 ARG 0.007 0.000 ARG F 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 457 time to evaluate : 5.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 ASP cc_start: 0.8159 (m-30) cc_final: 0.7920 (m-30) REVERT: E 339 ARG cc_start: 0.8380 (ptt180) cc_final: 0.8093 (ptp90) REVERT: F 254 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8445 (mtmt) REVERT: N 95 LYS cc_start: 0.7813 (mttm) cc_final: 0.7043 (mtmt) REVERT: N 100 LYS cc_start: 0.4907 (mmtp) cc_final: 0.4256 (ptmt) REVERT: J 168 GLU cc_start: 0.7282 (mp0) cc_final: 0.7057 (mt-10) REVERT: J 186 ASN cc_start: 0.8805 (m-40) cc_final: 0.8584 (m-40) REVERT: J 297 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7901 (tm-30) REVERT: J 425 MET cc_start: 0.8379 (tpp) cc_final: 0.8117 (tpp) REVERT: G 47 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8238 (mm-30) REVERT: G 75 MET cc_start: 0.8951 (mmt) cc_final: 0.8317 (mmt) REVERT: G 254 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8215 (mtmt) REVERT: L 230 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8468 (mp) REVERT: L 284 GLU cc_start: 0.8302 (pt0) cc_final: 0.7968 (pm20) REVERT: L 327 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8315 (m-30) REVERT: I 59 ASN cc_start: 0.8454 (m-40) cc_final: 0.8074 (p0) REVERT: I 254 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8379 (ttmt) REVERT: B 259 MET cc_start: 0.8688 (mmm) cc_final: 0.8406 (mmp) REVERT: B 278 ARG cc_start: 0.8921 (mmm160) cc_final: 0.8701 (mmm160) REVERT: M 32 TYR cc_start: 0.7200 (m-10) cc_final: 0.6840 (m-80) REVERT: M 34 LYS cc_start: 0.7404 (mmmt) cc_final: 0.6896 (mppt) REVERT: M 37 GLN cc_start: 0.7588 (mp10) cc_final: 0.7287 (mp10) REVERT: M 50 MET cc_start: 0.4381 (ppp) cc_final: 0.4124 (ppp) REVERT: M 95 LYS cc_start: 0.7762 (mttm) cc_final: 0.7210 (mmpt) REVERT: M 96 LEU cc_start: 0.6732 (OUTLIER) cc_final: 0.6407 (mp) REVERT: M 100 LYS cc_start: 0.5716 (mmtp) cc_final: 0.4931 (ptmt) REVERT: M 118 ASN cc_start: 0.4052 (m-40) cc_final: 0.3838 (m-40) REVERT: K 18 ASN cc_start: 0.7995 (OUTLIER) cc_final: 0.7596 (m110) REVERT: K 123 ARG cc_start: 0.8771 (tpp-160) cc_final: 0.8397 (tpp80) REVERT: K 127 ASP cc_start: 0.8561 (p0) cc_final: 0.8233 (m-30) REVERT: H 26 ASP cc_start: 0.8008 (t0) cc_final: 0.7614 (t0) REVERT: H 41 ASP cc_start: 0.7310 (p0) cc_final: 0.6965 (p0) REVERT: H 47 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7993 (mm-30) REVERT: H 299 LYS cc_start: 0.8785 (ptmt) cc_final: 0.8452 (tttp) REVERT: H 349 ASN cc_start: 0.8301 (m-40) cc_final: 0.7976 (t0) REVERT: H 435 TYR cc_start: 0.8926 (m-80) cc_final: 0.8637 (m-10) outliers start: 116 outliers final: 91 residues processed: 547 average time/residue: 0.5231 time to fit residues: 478.8053 Evaluate side-chains 509 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 411 time to evaluate : 5.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 327 ASP Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 163 LYS Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain L residue 54 SER Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 213 CYS Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 335 ILE Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 213 CYS Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 332 ILE Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 499 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 295 optimal weight: 7.9990 chunk 378 optimal weight: 2.9990 chunk 293 optimal weight: 0.9990 chunk 436 optimal weight: 1.9990 chunk 289 optimal weight: 10.0000 chunk 516 optimal weight: 3.9990 chunk 323 optimal weight: 7.9990 chunk 314 optimal weight: 0.9990 chunk 238 optimal weight: 6.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN E 88 HIS ** E 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 118 ASN C 18 ASN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 43998 Z= 0.187 Angle : 0.512 13.322 59746 Z= 0.257 Chirality : 0.041 0.230 6522 Planarity : 0.004 0.048 7776 Dihedral : 10.927 179.058 6148 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.77 % Allowed : 15.22 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.11), residues: 5388 helix: 1.66 (0.11), residues: 2442 sheet: 0.22 (0.18), residues: 780 loop : -0.58 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 346 HIS 0.010 0.001 HIS E 88 PHE 0.012 0.001 PHE I 377 TYR 0.021 0.001 TYR K 24 ARG 0.007 0.000 ARG F 278 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 442 time to evaluate : 6.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 ASP cc_start: 0.8154 (m-30) cc_final: 0.7904 (m-30) REVERT: E 339 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.8050 (ptp90) REVERT: F 254 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8486 (mtmt) REVERT: N 95 LYS cc_start: 0.7816 (mttm) cc_final: 0.7067 (mtmt) REVERT: N 100 LYS cc_start: 0.4907 (mmtp) cc_final: 0.4273 (ptmt) REVERT: J 168 GLU cc_start: 0.7254 (mp0) cc_final: 0.7038 (mt-10) REVERT: J 186 ASN cc_start: 0.8796 (m-40) cc_final: 0.8586 (m-40) REVERT: J 297 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7928 (tm-30) REVERT: J 425 MET cc_start: 0.8359 (tpp) cc_final: 0.8118 (tpp) REVERT: G 47 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8170 (mm-30) REVERT: G 75 MET cc_start: 0.8971 (mmt) cc_final: 0.8415 (mmt) REVERT: G 254 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8241 (mtmt) REVERT: L 127 ASP cc_start: 0.8405 (m-30) cc_final: 0.8147 (m-30) REVERT: L 230 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8476 (mp) REVERT: L 284 GLU cc_start: 0.8260 (pt0) cc_final: 0.7988 (pm20) REVERT: L 327 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8225 (m-30) REVERT: I 254 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8413 (ttmt) REVERT: I 372 LYS cc_start: 0.8681 (mttp) cc_final: 0.8479 (mtpp) REVERT: A 127 ASP cc_start: 0.8703 (m-30) cc_final: 0.8150 (m-30) REVERT: B 278 ARG cc_start: 0.8889 (mmm160) cc_final: 0.8670 (mmm160) REVERT: M 32 TYR cc_start: 0.7234 (m-10) cc_final: 0.6890 (m-80) REVERT: M 34 LYS cc_start: 0.7377 (mmmt) cc_final: 0.6870 (mppt) REVERT: M 37 GLN cc_start: 0.7573 (mp10) cc_final: 0.7293 (mp10) REVERT: M 48 MET cc_start: 0.6131 (ttp) cc_final: 0.5872 (tmm) REVERT: M 50 MET cc_start: 0.4255 (ppp) cc_final: 0.3958 (ppp) REVERT: M 95 LYS cc_start: 0.7763 (mttm) cc_final: 0.7198 (mmpt) REVERT: M 96 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6563 (mp) REVERT: M 100 LYS cc_start: 0.5674 (mmtp) cc_final: 0.4902 (ptmt) REVERT: K 18 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7514 (m110) REVERT: K 123 ARG cc_start: 0.8750 (tpp-160) cc_final: 0.8368 (tpp80) REVERT: K 127 ASP cc_start: 0.8576 (p0) cc_final: 0.8201 (m-30) REVERT: H 26 ASP cc_start: 0.7983 (t0) cc_final: 0.7577 (t0) REVERT: H 41 ASP cc_start: 0.7327 (p0) cc_final: 0.6999 (p0) REVERT: H 47 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8001 (mm-30) REVERT: H 299 LYS cc_start: 0.8772 (ptmt) cc_final: 0.8516 (tttp) REVERT: H 435 TYR cc_start: 0.8878 (m-80) cc_final: 0.8623 (m-10) outliers start: 128 outliers final: 95 residues processed: 540 average time/residue: 0.5312 time to fit residues: 481.4581 Evaluate side-chains 511 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 408 time to evaluate : 4.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 381 SER Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain N residue 20 MET Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 163 LYS Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 234 ILE Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 275 VAL Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 315 CYS Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 213 CYS Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 254 LYS Chi-restraints excluded: chain I residue 269 MET Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 302 MET Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 356 CYS Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 18 ASN Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 242 LEU Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 319 optimal weight: 1.9990 chunk 206 optimal weight: 0.3980 chunk 308 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 328 optimal weight: 3.9990 chunk 351 optimal weight: 0.9980 chunk 255 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 406 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 283 HIS N 118 ASN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 43998 Z= 0.163 Angle : 0.514 13.212 59746 Z= 0.256 Chirality : 0.041 0.216 6522 Planarity : 0.004 0.045 7776 Dihedral : 10.798 177.469 6145 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.60 % Allowed : 15.40 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.11), residues: 5388 helix: 1.70 (0.11), residues: 2432 sheet: 0.18 (0.18), residues: 798 loop : -0.47 (0.13), residues: 2158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 346 HIS 0.005 0.001 HIS A 309 PHE 0.013 0.001 PHE F 169 TYR 0.020 0.001 TYR K 24 ARG 0.007 0.000 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 452 time to evaluate : 5.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 ASP cc_start: 0.8042 (m-30) cc_final: 0.7798 (m-30) REVERT: E 339 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.8013 (ptp90) REVERT: F 254 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8426 (mtmt) REVERT: N 95 LYS cc_start: 0.7889 (mttm) cc_final: 0.7136 (mtmt) REVERT: N 100 LYS cc_start: 0.4753 (mmtp) cc_final: 0.4132 (ptmt) REVERT: J 124 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8252 (mmmt) REVERT: J 168 GLU cc_start: 0.7294 (mp0) cc_final: 0.7004 (mt-10) REVERT: J 297 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7946 (tm-30) REVERT: G 47 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8134 (mm-30) REVERT: G 75 MET cc_start: 0.9028 (mmt) cc_final: 0.8539 (mmt) REVERT: G 254 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8173 (mtmt) REVERT: C 50 ASN cc_start: 0.8854 (t0) cc_final: 0.8511 (t0) REVERT: D 373 MET cc_start: 0.7521 (ttp) cc_final: 0.7300 (ttp) REVERT: L 127 ASP cc_start: 0.8390 (m-30) cc_final: 0.8155 (m-30) REVERT: L 230 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8463 (mp) REVERT: L 284 GLU cc_start: 0.8275 (pt0) cc_final: 0.8039 (pm20) REVERT: L 297 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8052 (tm-30) REVERT: L 327 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8224 (m-30) REVERT: I 59 ASN cc_start: 0.8413 (m-40) cc_final: 0.8087 (p0) REVERT: I 299 LYS cc_start: 0.8797 (ptmt) cc_final: 0.8569 (tmtt) REVERT: I 315 VAL cc_start: 0.9174 (OUTLIER) cc_final: 0.8730 (m) REVERT: I 372 LYS cc_start: 0.8646 (mttp) cc_final: 0.8419 (mtpp) REVERT: A 154 MET cc_start: 0.8360 (mmm) cc_final: 0.8094 (mmm) REVERT: B 259 MET cc_start: 0.8632 (mmm) cc_final: 0.8067 (mmp) REVERT: B 278 ARG cc_start: 0.8873 (mmm160) cc_final: 0.8653 (mmm160) REVERT: M 32 TYR cc_start: 0.7230 (m-10) cc_final: 0.6927 (m-80) REVERT: M 34 LYS cc_start: 0.7384 (mmmt) cc_final: 0.6823 (mppt) REVERT: M 37 GLN cc_start: 0.7699 (mp10) cc_final: 0.7329 (mp10) REVERT: M 50 MET cc_start: 0.3957 (ppp) cc_final: 0.3657 (ppp) REVERT: M 95 LYS cc_start: 0.7744 (mttm) cc_final: 0.6913 (mtmt) REVERT: M 96 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6644 (mp) REVERT: M 100 LYS cc_start: 0.5542 (mmtp) cc_final: 0.4749 (ptmt) REVERT: K 123 ARG cc_start: 0.8755 (tpp-160) cc_final: 0.8353 (tpp80) REVERT: K 127 ASP cc_start: 0.8524 (p0) cc_final: 0.8192 (m-30) REVERT: K 425 MET cc_start: 0.8380 (tpp) cc_final: 0.8126 (tpp) REVERT: H 26 ASP cc_start: 0.7972 (t0) cc_final: 0.7567 (t0) REVERT: H 41 ASP cc_start: 0.7327 (p0) cc_final: 0.6902 (p0) REVERT: H 47 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7877 (mm-30) REVERT: H 299 LYS cc_start: 0.8775 (ptmt) cc_final: 0.8516 (tttp) REVERT: H 349 ASN cc_start: 0.8317 (m-40) cc_final: 0.8017 (t0) outliers start: 120 outliers final: 92 residues processed: 546 average time/residue: 0.5192 time to fit residues: 475.0318 Evaluate side-chains 515 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 416 time to evaluate : 4.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 163 LYS Chi-restraints excluded: chain J residue 165 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 327 ASP Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 213 CYS Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 36 MET Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 269 MET Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 469 optimal weight: 6.9990 chunk 494 optimal weight: 3.9990 chunk 451 optimal weight: 10.0000 chunk 481 optimal weight: 6.9990 chunk 289 optimal weight: 0.0470 chunk 209 optimal weight: 10.0000 chunk 378 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 435 optimal weight: 0.5980 chunk 455 optimal weight: 3.9990 chunk 479 optimal weight: 4.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 118 ASN D 107 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 43998 Z= 0.182 Angle : 0.523 13.572 59746 Z= 0.260 Chirality : 0.041 0.227 6522 Planarity : 0.004 0.049 7776 Dihedral : 10.759 177.197 6143 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.40 % Allowed : 15.81 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.91 (0.11), residues: 5388 helix: 1.71 (0.11), residues: 2430 sheet: 0.18 (0.18), residues: 798 loop : -0.46 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 346 HIS 0.003 0.001 HIS E 88 PHE 0.015 0.001 PHE H 377 TYR 0.031 0.001 TYR L 24 ARG 0.009 0.000 ARG D 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 433 time to evaluate : 4.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 ASP cc_start: 0.8156 (m-30) cc_final: 0.7903 (m-30) REVERT: E 339 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.8004 (ptp90) REVERT: F 254 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8392 (mtmt) REVERT: N 95 LYS cc_start: 0.7703 (mttm) cc_final: 0.7104 (mtmt) REVERT: N 100 LYS cc_start: 0.4998 (mmtp) cc_final: 0.4298 (ptmt) REVERT: J 123 ARG cc_start: 0.8676 (tpp80) cc_final: 0.8447 (tpp80) REVERT: J 127 ASP cc_start: 0.8365 (m-30) cc_final: 0.8151 (m-30) REVERT: J 168 GLU cc_start: 0.7288 (mp0) cc_final: 0.6983 (mt-10) REVERT: J 297 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7881 (tm-30) REVERT: G 47 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8133 (mm-30) REVERT: G 75 MET cc_start: 0.9015 (mmt) cc_final: 0.8724 (mmt) REVERT: G 254 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8223 (mtmt) REVERT: C 50 ASN cc_start: 0.8852 (t0) cc_final: 0.8524 (t0) REVERT: L 230 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8468 (mp) REVERT: L 284 GLU cc_start: 0.8326 (pt0) cc_final: 0.8055 (pm20) REVERT: L 327 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8209 (m-30) REVERT: I 59 ASN cc_start: 0.8419 (m-40) cc_final: 0.8094 (p0) REVERT: I 315 VAL cc_start: 0.9201 (OUTLIER) cc_final: 0.8780 (m) REVERT: I 372 LYS cc_start: 0.8668 (mttp) cc_final: 0.8459 (mtpp) REVERT: A 154 MET cc_start: 0.8364 (mmm) cc_final: 0.8116 (mmm) REVERT: B 47 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7694 (mp0) REVERT: B 278 ARG cc_start: 0.8877 (mmm160) cc_final: 0.8666 (mmm160) REVERT: B 323 MET cc_start: 0.7555 (OUTLIER) cc_final: 0.7034 (mtm) REVERT: M 32 TYR cc_start: 0.7233 (m-10) cc_final: 0.6907 (m-80) REVERT: M 34 LYS cc_start: 0.7357 (mmmt) cc_final: 0.6806 (mppt) REVERT: M 37 GLN cc_start: 0.7778 (mp10) cc_final: 0.7460 (mp10) REVERT: M 48 MET cc_start: 0.6400 (ttp) cc_final: 0.6169 (tmm) REVERT: M 50 MET cc_start: 0.3977 (ppp) cc_final: 0.3657 (ppp) REVERT: M 95 LYS cc_start: 0.7733 (mttm) cc_final: 0.6909 (mtmt) REVERT: M 96 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6681 (mp) REVERT: M 100 LYS cc_start: 0.5505 (mmtp) cc_final: 0.4763 (ptmt) REVERT: K 127 ASP cc_start: 0.8500 (p0) cc_final: 0.8225 (m-30) REVERT: K 172 TYR cc_start: 0.8433 (t80) cc_final: 0.8087 (t80) REVERT: K 425 MET cc_start: 0.8321 (tpp) cc_final: 0.8015 (tpp) REVERT: H 26 ASP cc_start: 0.7974 (t0) cc_final: 0.7566 (t0) REVERT: H 41 ASP cc_start: 0.7313 (p0) cc_final: 0.6905 (p0) REVERT: H 47 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7901 (mm-30) REVERT: H 299 LYS cc_start: 0.8772 (ptmt) cc_final: 0.8537 (tttp) REVERT: H 349 ASN cc_start: 0.8395 (m-40) cc_final: 0.8044 (t0) outliers start: 111 outliers final: 94 residues processed: 523 average time/residue: 0.5128 time to fit residues: 451.2519 Evaluate side-chains 520 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 418 time to evaluate : 4.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 253 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 86 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 213 CYS Chi-restraints excluded: chain G residue 242 LEU Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 158 SER Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 230 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 288 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 213 CYS Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 286 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 381 THR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 93 VAL Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 316 optimal weight: 4.9990 chunk 509 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 241 optimal weight: 0.9980 chunk 353 optimal weight: 10.0000 chunk 533 optimal weight: 0.4980 chunk 491 optimal weight: 0.9990 chunk 425 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 328 optimal weight: 3.9990 chunk 260 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 37 GLN N 118 ASN C 88 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 331 GLN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 ASN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 43998 Z= 0.156 Angle : 0.520 13.091 59746 Z= 0.257 Chirality : 0.041 0.224 6522 Planarity : 0.004 0.050 7776 Dihedral : 10.691 178.009 6143 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.21 % Allowed : 16.13 % Favored : 81.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.94 (0.11), residues: 5388 helix: 1.71 (0.11), residues: 2430 sheet: 0.23 (0.18), residues: 798 loop : -0.43 (0.13), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 346 HIS 0.003 0.001 HIS E 283 PHE 0.014 0.001 PHE H 377 TYR 0.026 0.001 TYR L 24 ARG 0.012 0.000 ARG D 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10776 Ramachandran restraints generated. 5388 Oldfield, 0 Emsley, 5388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 446 time to evaluate : 5.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 120 ASP cc_start: 0.8056 (m-30) cc_final: 0.7792 (m-30) REVERT: E 339 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7962 (ptp90) REVERT: F 254 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8388 (mtmt) REVERT: F 323 MET cc_start: 0.7859 (OUTLIER) cc_final: 0.7308 (mtp) REVERT: N 95 LYS cc_start: 0.7661 (mttm) cc_final: 0.7091 (mtmt) REVERT: N 100 LYS cc_start: 0.4995 (mmtp) cc_final: 0.4294 (ptmt) REVERT: J 168 GLU cc_start: 0.7267 (mp0) cc_final: 0.6979 (mt-10) REVERT: J 297 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7897 (tm-30) REVERT: G 47 GLU cc_start: 0.8448 (mm-30) cc_final: 0.8138 (mm-30) REVERT: G 75 MET cc_start: 0.8997 (mmt) cc_final: 0.8759 (mmt) REVERT: G 170 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8674 (p) REVERT: G 254 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8177 (mtmt) REVERT: G 323 MET cc_start: 0.9035 (pmm) cc_final: 0.7681 (ptp) REVERT: C 50 ASN cc_start: 0.8840 (t0) cc_final: 0.8502 (t0) REVERT: D 278 ARG cc_start: 0.8966 (mmm160) cc_final: 0.8377 (mmm160) REVERT: D 308 ARG cc_start: 0.8142 (mtt90) cc_final: 0.7219 (mtm-85) REVERT: L 127 ASP cc_start: 0.8302 (m-30) cc_final: 0.8002 (m-30) REVERT: L 275 VAL cc_start: 0.9046 (OUTLIER) cc_final: 0.8739 (p) REVERT: L 284 GLU cc_start: 0.8265 (pt0) cc_final: 0.8041 (pm20) REVERT: L 297 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8091 (tm-30) REVERT: L 327 ASP cc_start: 0.8439 (OUTLIER) cc_final: 0.8202 (m-30) REVERT: I 59 ASN cc_start: 0.8393 (m-40) cc_final: 0.8085 (p0) REVERT: I 315 VAL cc_start: 0.9152 (OUTLIER) cc_final: 0.8727 (m) REVERT: A 127 ASP cc_start: 0.8661 (m-30) cc_final: 0.8248 (m-30) REVERT: A 154 MET cc_start: 0.8332 (mmm) cc_final: 0.8096 (mmm) REVERT: B 47 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7672 (mp0) REVERT: B 323 MET cc_start: 0.7613 (mtm) cc_final: 0.6950 (mtm) REVERT: M 32 TYR cc_start: 0.7161 (m-10) cc_final: 0.6617 (m-80) REVERT: M 34 LYS cc_start: 0.7320 (mmmt) cc_final: 0.6913 (mppt) REVERT: M 37 GLN cc_start: 0.7758 (mp10) cc_final: 0.7188 (mt0) REVERT: M 50 MET cc_start: 0.4076 (ppp) cc_final: 0.3698 (ppp) REVERT: M 95 LYS cc_start: 0.7686 (mttm) cc_final: 0.6874 (mtmt) REVERT: M 96 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6668 (mp) REVERT: M 100 LYS cc_start: 0.5474 (mmtp) cc_final: 0.4756 (ptmt) REVERT: K 127 ASP cc_start: 0.8509 (p0) cc_final: 0.8226 (m-30) REVERT: K 172 TYR cc_start: 0.8349 (t80) cc_final: 0.7872 (t80) REVERT: K 425 MET cc_start: 0.8331 (tpp) cc_final: 0.8036 (tpp) REVERT: H 26 ASP cc_start: 0.7944 (t0) cc_final: 0.7565 (t0) REVERT: H 41 ASP cc_start: 0.7324 (p0) cc_final: 0.6906 (p0) REVERT: H 47 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7900 (mm-30) REVERT: H 299 LYS cc_start: 0.8689 (ptmt) cc_final: 0.8448 (tttp) outliers start: 102 outliers final: 86 residues processed: 528 average time/residue: 0.5229 time to fit residues: 463.7446 Evaluate side-chains 514 residues out of total 4644 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 419 time to evaluate : 4.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 223 THR Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 339 ARG Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 363 VAL Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 97 SER Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 138 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 254 LYS Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 299 LYS Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 356 CYS Chi-restraints excluded: chain F residue 414 ASP Chi-restraints excluded: chain J residue 54 SER Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 253 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 288 VAL Chi-restraints excluded: chain J residue 332 ILE Chi-restraints excluded: chain J residue 363 VAL Chi-restraints excluded: chain J residue 367 ASP Chi-restraints excluded: chain J residue 381 THR Chi-restraints excluded: chain J residue 435 VAL Chi-restraints excluded: chain G residue 12 CYS Chi-restraints excluded: chain G residue 93 VAL Chi-restraints excluded: chain G residue 114 LEU Chi-restraints excluded: chain G residue 145 THR Chi-restraints excluded: chain G residue 167 ASN Chi-restraints excluded: chain G residue 170 SER Chi-restraints excluded: chain G residue 254 LYS Chi-restraints excluded: chain G residue 314 THR Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 279 GLU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 414 ASP Chi-restraints excluded: chain L residue 124 LYS Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 190 THR Chi-restraints excluded: chain L residue 223 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 327 ASP Chi-restraints excluded: chain L residue 362 VAL Chi-restraints excluded: chain L residue 363 VAL Chi-restraints excluded: chain L residue 367 ASP Chi-restraints excluded: chain L residue 381 THR Chi-restraints excluded: chain I residue 12 CYS Chi-restraints excluded: chain I residue 33 THR Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 213 CYS Chi-restraints excluded: chain I residue 242 LEU Chi-restraints excluded: chain I residue 315 VAL Chi-restraints excluded: chain A residue 36 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 367 ASP Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 101 ASN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 145 THR Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 414 ASP Chi-restraints excluded: chain M residue 96 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 190 THR Chi-restraints excluded: chain K residue 362 VAL Chi-restraints excluded: chain K residue 363 VAL Chi-restraints excluded: chain K residue 367 ASP Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 12 CYS Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 137 LEU Chi-restraints excluded: chain H residue 232 SER Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 414 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 337 optimal weight: 4.9990 chunk 452 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 392 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 425 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 437 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 37 GLN N 118 ASN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 101 ASN ** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 GLN ** K 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.088206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.073136 restraints weight = 90927.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.075630 restraints weight = 42647.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077313 restraints weight = 25772.351| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 43998 Z= 0.260 Angle : 0.550 12.496 59746 Z= 0.274 Chirality : 0.042 0.232 6522 Planarity : 0.004 0.056 7776 Dihedral : 10.763 178.714 6142 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.30 % Allowed : 16.07 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.88 % 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: 0.89 (0.11), residues: 5388 helix: 1.65 (0.11), residues: 2460 sheet: 0.34 (0.18), residues: 762 loop : -0.51 (0.13), residues: 2166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 346 HIS 0.004 0.001 HIS E 283 PHE 0.014 0.001 PHE H 377 TYR 0.022 0.001 TYR K 24 ARG 0.009 0.000 ARG B 278 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9625.90 seconds wall clock time: 175 minutes 22.05 seconds (10522.05 seconds total)