Starting phenix.real_space_refine on Sun Mar 24 07:37:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jat_6352/03_2024/3jat_6352_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jat_6352/03_2024/3jat_6352.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/3jat_6352/03_2024/3jat_6352.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jat_6352/03_2024/3jat_6352.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jat_6352/03_2024/3jat_6352_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3jat_6352/03_2024/3jat_6352_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= 0.043 sd= 0.912 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 36 5.49 5 Mg 12 5.21 5 S 276 5.16 5 C 25464 2.51 5 N 6918 2.21 5 O 7794 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ARG 64": "NH1" <-> "NH2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E ARG 320": "NH1" <-> "NH2" Residue "E GLU 411": "OE1" <-> "OE2" Residue "E GLU 414": "OE1" <-> "OE2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "F GLU 417": "OE1" <-> "OE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 84": "NH1" <-> "NH2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 279": "OE1" <-> "OE2" Residue "J ARG 320": "NH1" <-> "NH2" Residue "J GLU 411": "OE1" <-> "OE2" Residue "J GLU 414": "OE1" <-> "OE2" Residue "J GLU 429": "OE1" <-> "OE2" Residue "J GLU 433": "OE1" <-> "OE2" Residue "G GLU 417": "OE1" <-> "OE2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 84": "NH1" <-> "NH2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C ARG 320": "NH1" <-> "NH2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C GLU 414": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "D GLU 417": "OE1" <-> "OE2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 84": "NH1" <-> "NH2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 279": "OE1" <-> "OE2" Residue "L ARG 320": "NH1" <-> "NH2" Residue "L GLU 411": "OE1" <-> "OE2" Residue "L GLU 414": "OE1" <-> "OE2" Residue "L GLU 429": "OE1" <-> "OE2" Residue "L GLU 433": "OE1" <-> "OE2" Residue "I GLU 417": "OE1" <-> "OE2" Residue "A ARG 64": "NH1" <-> "NH2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 279": "OE1" <-> "OE2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A GLU 411": "OE1" <-> "OE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 84": "NH1" <-> "NH2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K GLU 279": "OE1" <-> "OE2" Residue "K ARG 320": "NH1" <-> "NH2" Residue "K GLU 411": "OE1" <-> "OE2" Residue "K GLU 414": "OE1" <-> "OE2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "K GLU 433": "OE1" <-> "OE2" Residue "H GLU 417": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 40500 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "G" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "D" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3342 Classifications: {'peptide': 428} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 3342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3342 Classifications: {'peptide': 426} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'G2P': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 19.74, per 1000 atoms: 0.49 Number of scatterers: 40500 At special positions: 0 Unit cell: (174.24, 88.44, 211.2, 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 276 16.00 P 36 15.00 Mg 12 11.99 O 7794 8.00 N 6918 7.00 C 25464 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: 16.02 Conformation dependent library (CDL) restraints added in 7.2 seconds 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9492 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 252 helices and 36 sheets defined 50.1% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.36 Creating SS restraints... Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 73 through 80 removed outlier: 3.608A 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: 3.558A pdb=" N GLN E 128 " --> pdb=" O LYS E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 160 removed outlier: 4.079A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.583A pdb=" N HIS E 192 " --> pdb=" O ILE E 188 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 224 through 243 removed outlier: 4.405A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 278 through 283 removed outlier: 3.995A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HIS E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 278 through 283' Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.602A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) 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: 3.540A pdb=" N TYR E 399 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 Processing helix chain 'E' and resid 415 through 436 Processing helix chain 'F' and resid 11 through 27 Processing helix chain 'F' and resid 41 through 47 removed outlier: 3.555A 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 72 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 108 Processing helix chain 'F' and resid 110 through 128 removed outlier: 4.295A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 160 Processing helix chain 'F' and resid 183 through 197 removed outlier: 3.546A pdb=" N GLN F 193 " --> pdb=" O LEU F 189 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.812A pdb=" N THR F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 5.736A 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 279 through 281 No H-bonds generated for 'chain 'F' and resid 279 through 281' Processing helix chain 'F' and resid 288 through 296 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: 3.769A pdb=" N ARG F 390 " --> pdb=" O LEU F 387 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG F 400 " --> pdb=" O ALA F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 411 Processing helix chain 'F' and resid 415 through 435 Processing helix chain 'J' and resid 10 through 28 Processing helix chain 'J' and resid 48 through 51 Processing helix chain 'J' and resid 73 through 80 removed outlier: 3.608A 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: 3.559A pdb=" N GLN J 128 " --> pdb=" O LYS J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 160 removed outlier: 4.080A pdb=" N THR J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 197 removed outlier: 3.583A pdb=" N HIS J 192 " --> pdb=" O ILE J 188 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N THR J 193 " --> pdb=" O LEU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 217 Processing helix chain 'J' and resid 224 through 243 removed outlier: 4.406A pdb=" N SER J 241 " --> pdb=" O SER J 237 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU J 242 " --> pdb=" O ILE J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 Processing helix chain 'J' and resid 278 through 283 removed outlier: 3.993A pdb=" N TYR J 282 " --> pdb=" O ALA J 278 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 278 through 283' Processing helix chain 'J' and resid 288 through 296 removed outlier: 3.603A pdb=" N PHE J 296 " --> pdb=" O THR J 292 " (cutoff:3.500A) 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: 3.541A pdb=" N TYR J 399 " --> pdb=" O ASP J 396 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 411 Processing helix chain 'J' and resid 415 through 436 Processing helix chain 'G' and resid 11 through 27 Processing helix chain 'G' and resid 41 through 47 removed outlier: 3.555A 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 72 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 108 Processing helix chain 'G' and resid 110 through 128 removed outlier: 4.293A pdb=" N ASP G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 160 Processing helix chain 'G' and resid 183 through 197 removed outlier: 3.545A pdb=" N GLN G 193 " --> pdb=" O LEU G 189 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.812A pdb=" N THR G 239 " --> pdb=" O MET G 235 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N CYS G 241 " --> pdb=" O GLY G 237 " (cutoff:3.500A) removed outlier: 5.735A 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 279 through 281 No H-bonds generated for 'chain 'G' and resid 279 through 281' Processing helix chain 'G' and resid 288 through 296 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: 3.768A pdb=" N ARG G 390 " --> pdb=" O LEU G 387 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG G 400 " --> pdb=" O ALA G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 411 Processing helix chain 'G' and resid 415 through 435 Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 48 through 51 Processing helix chain 'C' and resid 73 through 80 removed outlier: 3.608A 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: 3.557A pdb=" N GLN C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 160 removed outlier: 4.079A pdb=" N THR C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.584A pdb=" N HIS C 192 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR C 193 " --> pdb=" O LEU C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 224 through 243 removed outlier: 4.406A pdb=" N SER C 241 " --> pdb=" O SER C 237 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU C 242 " --> pdb=" O ILE C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 278 through 283 removed outlier: 3.996A pdb=" N TYR C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N HIS C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 278 through 283' Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.603A pdb=" N PHE C 296 " --> pdb=" O THR C 292 " (cutoff:3.500A) 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: 3.539A pdb=" N TYR C 399 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 Processing helix chain 'C' and resid 415 through 436 Processing helix chain 'D' and resid 11 through 27 Processing helix chain 'D' and resid 41 through 47 removed outlier: 3.556A 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 72 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 108 Processing helix chain 'D' and resid 110 through 128 removed outlier: 4.296A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 160 Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.545A pdb=" N GLN D 193 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.813A pdb=" N THR D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 5.736A 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 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 288 through 296 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: 3.770A pdb=" N ARG D 390 " --> pdb=" O LEU D 387 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG D 400 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 411 Processing helix chain 'D' and resid 415 through 435 Processing helix chain 'L' and resid 10 through 28 Processing helix chain 'L' and resid 48 through 51 Processing helix chain 'L' and resid 73 through 80 removed outlier: 3.609A 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: 3.557A pdb=" N GLN L 128 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 144 through 160 removed outlier: 4.082A pdb=" N THR L 150 " --> pdb=" O GLY L 146 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 197 removed outlier: 3.583A pdb=" N HIS L 192 " --> pdb=" O ILE L 188 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR L 193 " --> pdb=" O LEU L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 217 Processing helix chain 'L' and resid 224 through 243 removed outlier: 4.406A pdb=" N SER L 241 " --> pdb=" O SER L 237 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU L 242 " --> pdb=" O ILE L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 259 Processing helix chain 'L' and resid 278 through 283 removed outlier: 3.994A pdb=" N TYR L 282 " --> pdb=" O ALA L 278 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 278 through 283' Processing helix chain 'L' and resid 288 through 296 removed outlier: 3.603A pdb=" N PHE L 296 " --> pdb=" O THR L 292 " (cutoff:3.500A) 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: 3.541A pdb=" N TYR L 399 " --> pdb=" O ASP L 396 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 411 Processing helix chain 'L' and resid 415 through 436 Processing helix chain 'I' and resid 11 through 27 Processing helix chain 'I' and resid 41 through 47 removed outlier: 3.555A 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 72 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 108 Processing helix chain 'I' and resid 110 through 128 removed outlier: 4.295A pdb=" N ASP I 116 " --> pdb=" O ALA I 112 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N SER I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 160 Processing helix chain 'I' and resid 183 through 197 removed outlier: 3.545A pdb=" N GLN I 193 " --> pdb=" O LEU I 189 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.813A pdb=" N THR I 239 " --> pdb=" O MET I 235 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N CYS I 241 " --> pdb=" O GLY I 237 " (cutoff:3.500A) removed outlier: 5.736A 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 279 through 281 No H-bonds generated for 'chain 'I' and resid 279 through 281' Processing helix chain 'I' and resid 288 through 296 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: 3.769A pdb=" N ARG I 390 " --> pdb=" O LEU I 387 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG I 400 " --> pdb=" O ALA I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 411 Processing helix chain 'I' and resid 415 through 435 Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 73 through 80 removed outlier: 3.608A 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: 3.558A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.078A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.584A pdb=" N HIS A 192 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 224 through 243 removed outlier: 4.406A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.995A pdb=" N TYR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 288 through 296 removed outlier: 3.602A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) 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: 3.539A pdb=" N TYR A 399 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 11 through 27 Processing helix chain 'B' and resid 41 through 47 removed outlier: 3.555A 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 72 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 108 Processing helix chain 'B' and resid 110 through 128 removed outlier: 4.295A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 160 Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.545A pdb=" N GLN B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.603A 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: 3.813A pdb=" N THR B 239 " --> pdb=" O MET B 235 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 5.736A 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 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 288 through 296 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: 3.770A pdb=" N ARG B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ARG B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 Processing helix chain 'B' and resid 415 through 435 Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 48 through 51 Processing helix chain 'K' and resid 73 through 80 removed outlier: 3.609A 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: 3.558A pdb=" N GLN K 128 " --> pdb=" O LYS K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 160 removed outlier: 4.081A pdb=" N THR K 150 " --> pdb=" O GLY K 146 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 197 removed outlier: 3.583A pdb=" N HIS K 192 " --> pdb=" O ILE K 188 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR K 193 " --> pdb=" O LEU K 189 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 217 Processing helix chain 'K' and resid 224 through 243 removed outlier: 4.406A pdb=" N SER K 241 " --> pdb=" O SER K 237 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LEU K 242 " --> pdb=" O ILE K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 278 through 283 removed outlier: 3.993A pdb=" N TYR K 282 " --> pdb=" O ALA K 278 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 278 through 283' Processing helix chain 'K' and resid 288 through 296 removed outlier: 3.603A pdb=" N PHE K 296 " --> pdb=" O THR K 292 " (cutoff:3.500A) 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: 3.540A pdb=" N TYR K 399 " --> pdb=" O ASP K 396 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 411 Processing helix chain 'K' and resid 415 through 436 Processing helix chain 'H' and resid 11 through 27 Processing helix chain 'H' and resid 41 through 47 removed outlier: 3.555A 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 72 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 108 Processing helix chain 'H' and resid 110 through 128 removed outlier: 4.295A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 160 Processing helix chain 'H' and resid 183 through 197 removed outlier: 3.545A pdb=" N GLN H 193 " --> pdb=" O LEU H 189 " (cutoff:3.500A) removed outlier: 3.602A 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: 3.813A pdb=" N THR H 239 " --> pdb=" O MET H 235 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 5.737A 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 279 through 281 No H-bonds generated for 'chain 'H' and resid 279 through 281' Processing helix chain 'H' and resid 288 through 296 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: 3.769A pdb=" N ARG H 390 " --> pdb=" O LEU H 387 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG H 400 " --> pdb=" O ALA H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 411 Processing helix chain 'H' and resid 415 through 435 Processing sheet with id= A, first strand: chain 'E' and resid 92 through 94 removed outlier: 8.019A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY E 131 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE E 5 " --> pdb=" O GLY E 131 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N GLN E 133 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 12.391A pdb=" N ILE E 7 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N PHE E 135 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 11.688A pdb=" N VAL E 9 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N VAL E 137 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.832A 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: 6.739A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 6.009A 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 269 through 273 removed outlier: 3.632A 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: 7.910A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.724A 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: 6.146A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL F 5 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE F 7 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA F 9 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS F 139 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU F 137 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.909A 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: 6.033A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU F 200 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER F 170 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL F 172 " --> pdb=" O TYR F 202 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE F 204 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 53 through 56 removed outlier: 3.892A pdb=" N LYS F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 269 through 273 Processing sheet with id= G, first strand: chain 'J' and resid 92 through 94 removed outlier: 8.017A pdb=" N ILE J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE J 67 " --> pdb=" O ILE J 93 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL J 66 " --> pdb=" O CYS J 4 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER J 6 " --> pdb=" O VAL J 66 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL J 68 " --> pdb=" O SER J 6 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N HIS J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY J 131 " --> pdb=" O GLU J 3 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE J 5 " --> pdb=" O GLY J 131 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N GLN J 133 " --> pdb=" O ILE J 5 " (cutoff:3.500A) removed outlier: 12.388A pdb=" N ILE J 7 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N PHE J 135 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 11.687A pdb=" N VAL J 9 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N VAL J 137 " --> pdb=" O VAL J 9 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N VAL J 137 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LEU J 167 " --> pdb=" O VAL J 137 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N HIS J 139 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N PHE J 169 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS J 200 " --> pdb=" O GLU J 168 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER J 170 " --> pdb=" O CYS J 200 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR J 172 " --> pdb=" O PHE J 202 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL J 204 " --> pdb=" O TYR J 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'J' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'J' and resid 269 through 273 removed outlier: 3.632A pdb=" N ALA J 314 " --> pdb=" O ASN J 380 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.909A pdb=" N VAL G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU G 67 " --> pdb=" O VAL G 93 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE G 66 " --> pdb=" O ILE G 4 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N HIS G 6 " --> pdb=" O ILE G 66 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL G 68 " --> pdb=" O HIS G 6 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLN G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL G 5 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE G 135 " --> pdb=" O VAL G 5 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE G 7 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA G 9 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS G 139 " --> pdb=" O ALA G 9 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE G 165 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU G 137 " --> pdb=" O ILE G 165 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ASN G 167 " --> pdb=" O LEU G 137 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N HIS G 139 " --> pdb=" O ASN G 167 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N PHE G 169 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU G 200 " --> pdb=" O THR G 168 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER G 170 " --> pdb=" O GLU G 200 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL G 172 " --> pdb=" O TYR G 202 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE G 204 " --> pdb=" O VAL G 172 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'G' and resid 53 through 56 removed outlier: 3.893A pdb=" N LYS G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 269 through 273 Processing sheet with id= M, first strand: chain 'C' and resid 92 through 94 removed outlier: 8.021A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY C 131 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ILE C 5 " --> pdb=" O GLY C 131 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N GLN C 133 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N ILE C 7 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N PHE C 135 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N VAL C 9 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N VAL C 137 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'C' and resid 269 through 273 removed outlier: 3.632A pdb=" N ALA C 314 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.909A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.724A 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: 6.145A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL D 5 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE D 7 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA D 9 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS D 139 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU D 137 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N HIS D 139 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU D 200 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER D 170 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR D 202 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL D 172 " --> pdb=" O TYR D 202 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE D 204 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 53 through 56 removed outlier: 3.892A pdb=" N LYS D 60 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 269 through 273 Processing sheet with id= S, first strand: chain 'L' and resid 92 through 94 removed outlier: 8.020A pdb=" N ILE L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE L 67 " --> pdb=" O ILE L 93 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N VAL L 66 " --> pdb=" O CYS L 4 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER L 6 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL L 68 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N HIS L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY L 131 " --> pdb=" O GLU L 3 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N ILE L 5 " --> pdb=" O GLY L 131 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLN L 133 " --> pdb=" O ILE L 5 " (cutoff:3.500A) removed outlier: 12.390A pdb=" N ILE L 7 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 9.418A pdb=" N PHE L 135 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 11.687A pdb=" N VAL L 9 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 9.596A pdb=" N VAL L 137 " --> pdb=" O VAL L 9 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N VAL L 137 " --> pdb=" O SER L 165 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU L 167 " --> pdb=" O VAL L 137 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N HIS L 139 " --> pdb=" O LEU L 167 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE L 169 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS L 200 " --> pdb=" O GLU L 168 " (cutoff:3.500A) removed outlier: 8.077A pdb=" N SER L 170 " --> pdb=" O CYS L 200 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N PHE L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR L 172 " --> pdb=" O PHE L 202 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL L 204 " --> pdb=" O TYR L 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'L' and resid 53 through 55 Processing sheet with id= U, first strand: chain 'L' and resid 269 through 273 removed outlier: 3.631A pdb=" N ALA L 314 " --> pdb=" O ASN L 380 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.909A pdb=" N VAL I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N LEU I 67 " --> pdb=" O VAL I 93 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE I 66 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N HIS I 6 " --> pdb=" O ILE I 66 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL I 68 " --> pdb=" O HIS I 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N VAL I 5 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE I 135 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE I 7 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA I 9 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N HIS I 139 " --> pdb=" O ALA I 9 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE I 165 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU I 137 " --> pdb=" O ILE I 165 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN I 167 " --> pdb=" O LEU I 137 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N HIS I 139 " --> pdb=" O ASN I 167 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU I 200 " --> pdb=" O THR I 168 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER I 170 " --> pdb=" O GLU I 200 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N TYR I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL I 172 " --> pdb=" O TYR I 202 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE I 204 " --> pdb=" O VAL I 172 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'I' and resid 53 through 56 removed outlier: 3.891A pdb=" N LYS I 60 " --> pdb=" O ALA I 56 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'I' and resid 269 through 273 Processing sheet with id= Y, first strand: chain 'A' and resid 92 through 94 removed outlier: 8.020A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.382A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY A 131 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ILE A 5 " --> pdb=" O GLY A 131 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N GLN A 133 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 12.393A pdb=" N ILE A 7 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N PHE A 135 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 11.687A pdb=" N VAL A 9 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N VAL A 137 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= AA, first strand: chain 'A' and resid 269 through 273 removed outlier: 3.632A pdb=" N ALA A 314 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.910A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 172 " --> pdb=" O TYR B 202 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE B 204 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'B' and resid 53 through 56 removed outlier: 3.893A pdb=" N LYS B 60 " --> pdb=" O ALA B 56 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'B' and resid 269 through 273 Processing sheet with id= AE, first strand: chain 'K' and resid 92 through 94 removed outlier: 8.018A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY K 131 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N ILE K 5 " --> pdb=" O GLY K 131 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N GLN K 133 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 12.390A pdb=" N ILE K 7 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 9.417A pdb=" N PHE K 135 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 11.686A pdb=" N VAL K 9 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 9.597A pdb=" N VAL K 137 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 8.075A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AG, first strand: chain 'K' and resid 269 through 273 removed outlier: 3.632A pdb=" N ALA K 314 " --> pdb=" O ASN K 380 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.910A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.473A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE H 7 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ALA H 9 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU H 137 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ASN H 167 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N HIS H 139 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU H 200 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N SER H 170 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL H 172 " --> pdb=" O TYR H 202 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE H 204 " --> pdb=" O VAL H 172 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 53 through 56 removed outlier: 3.892A pdb=" N LYS H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 269 through 273 1788 hydrogen bonds defined for protein. 4734 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: 15.01 Time building geometry restraints manager: 17.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7613 1.33 - 1.45: 10709 1.45 - 1.57: 22598 1.57 - 1.70: 60 1.70 - 1.82: 444 Bond restraints: 41424 Sorted by residual: bond pdb=" O3B G2P B 501 " pdb=" PG G2P B 501 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" O3B G2P D 501 " pdb=" PG G2P D 501 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" O3B G2P H 501 " pdb=" PG G2P H 501 " ideal model delta sigma weight residual 1.716 1.610 0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" O3B G2P I 501 " pdb=" PG G2P I 501 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" O3B G2P F 501 " pdb=" PG G2P F 501 " ideal model delta sigma weight residual 1.716 1.611 0.105 2.00e-02 2.50e+03 2.75e+01 ... (remaining 41419 not shown) Histogram of bond angle deviations from ideal: 94.43 - 103.08: 392 103.08 - 111.72: 16531 111.72 - 120.37: 22590 120.37 - 129.01: 16474 129.01 - 137.66: 305 Bond angle restraints: 56292 Sorted by residual: angle pdb=" N HIS E 197 " pdb=" CA HIS E 197 " pdb=" C HIS E 197 " ideal model delta sigma weight residual 111.02 119.44 -8.42 1.52e+00 4.33e-01 3.07e+01 angle pdb=" N HIS A 197 " pdb=" CA HIS A 197 " pdb=" C HIS A 197 " ideal model delta sigma weight residual 111.02 119.40 -8.38 1.52e+00 4.33e-01 3.04e+01 angle pdb=" N HIS C 197 " pdb=" CA HIS C 197 " pdb=" C HIS C 197 " ideal model delta sigma weight residual 111.02 119.36 -8.34 1.52e+00 4.33e-01 3.01e+01 angle pdb=" N HIS J 197 " pdb=" CA HIS J 197 " pdb=" C HIS J 197 " ideal model delta sigma weight residual 111.02 119.36 -8.34 1.52e+00 4.33e-01 3.01e+01 angle pdb=" N HIS L 197 " pdb=" CA HIS L 197 " pdb=" C HIS L 197 " ideal model delta sigma weight residual 111.02 119.34 -8.32 1.52e+00 4.33e-01 3.00e+01 ... (remaining 56287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.66: 23941 33.66 - 67.31: 684 67.31 - 100.97: 77 100.97 - 134.63: 0 134.63 - 168.29: 18 Dihedral angle restraints: 24720 sinusoidal: 9918 harmonic: 14802 Sorted by residual: 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 -122.45 -168.29 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.53 -168.20 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" C5' GTP C 501 " pdb=" O5' GTP C 501 " pdb=" PA GTP C 501 " pdb=" O3A GTP C 501 " ideal model delta sinusoidal sigma weight residual 69.27 -122.56 -168.17 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 24717 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4545 0.087 - 0.174: 1206 0.174 - 0.262: 344 0.262 - 0.349: 53 0.349 - 0.436: 8 Chirality restraints: 6156 Sorted by residual: 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 -2.27 -0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" C3' G2P G 501 " pdb=" C2' G2P G 501 " pdb=" C4' G2P G 501 " pdb=" O3' G2P G 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.28 -0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA HIS C 197 " pdb=" N HIS C 197 " pdb=" C HIS C 197 " pdb=" CB HIS C 197 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 6153 not shown) Planarity restraints: 7320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 288 " 0.049 5.00e-02 4.00e+02 7.46e-02 8.91e+00 pdb=" N PRO B 289 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO B 289 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 289 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 288 " 0.049 5.00e-02 4.00e+02 7.44e-02 8.86e+00 pdb=" N PRO D 289 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO D 289 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 289 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 288 " 0.049 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO F 289 " -0.128 5.00e-02 4.00e+02 pdb=" CA PRO F 289 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 289 " 0.041 5.00e-02 4.00e+02 ... (remaining 7317 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.46: 43 2.46 - 3.07: 26073 3.07 - 3.68: 63001 3.68 - 4.29: 90993 4.29 - 4.90: 157748 Nonbonded interactions: 337858 Sorted by model distance: nonbonded pdb=" O1B GTP J 501 " pdb="MG MG J 502 " model vdw 1.855 2.170 nonbonded pdb=" O1B GTP K 501 " pdb="MG MG K 502 " model vdw 1.862 2.170 nonbonded pdb=" O1B GTP E 501 " pdb="MG MG E 502 " model vdw 1.867 2.170 nonbonded pdb=" O1B GTP L 501 " pdb="MG MG L 502 " model vdw 1.883 2.170 nonbonded pdb=" O1B GTP A 501 " pdb="MG MG A 502 " model vdw 1.898 2.170 ... (remaining 337853 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' } 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: 7.150 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: 0.040 Extract box with map and model: 28.860 Check model and map are aligned: 0.460 Set scattering table: 0.300 Process input model: 103.120 Find NCS groups from input model: 2.510 Set up NCS constraints: 0.330 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 0.106 41424 Z= 0.614 Angle : 1.538 15.647 56292 Z= 1.046 Chirality : 0.089 0.436 6156 Planarity : 0.007 0.075 7320 Dihedral : 16.373 168.286 15228 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.07 % Favored : 96.82 % Rotamer: Outliers : 0.55 % Allowed : 7.13 % Favored : 92.31 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.11), residues: 5088 helix: 1.05 (0.09), residues: 2304 sheet: 0.34 (0.19), residues: 822 loop : -1.13 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 21 HIS 0.014 0.002 HIS A 88 PHE 0.022 0.003 PHE B 377 TYR 0.022 0.003 TYR G 224 ARG 0.023 0.001 ARG F 2 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 899 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 875 time to evaluate : 4.221 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: E 172 TYR cc_start: 0.7591 (t80) cc_final: 0.7020 (t80) REVERT: E 398 MET cc_start: 0.7845 (tpp) cc_final: 0.7422 (mtp) REVERT: J 178 SER cc_start: 0.7599 (OUTLIER) cc_final: 0.7327 (p) REVERT: J 210 TYR cc_start: 0.7514 (m-80) cc_final: 0.6962 (m-80) REVERT: J 357 TYR cc_start: 0.7090 (m-80) cc_final: 0.6831 (m-10) REVERT: G 114 LEU cc_start: 0.8989 (tp) cc_final: 0.8723 (tp) REVERT: G 166 MET cc_start: 0.7309 (tpp) cc_final: 0.7007 (tpp) REVERT: G 183 GLU cc_start: 0.7963 (tt0) cc_final: 0.7431 (tt0) REVERT: G 302 MET cc_start: 0.7186 (mtt) cc_final: 0.6948 (mtt) REVERT: G 325 MET cc_start: 0.7264 (mmm) cc_final: 0.6832 (mmm) REVERT: G 398 MET cc_start: 0.8296 (mmt) cc_final: 0.8047 (mmp) REVERT: C 259 LEU cc_start: 0.8923 (tp) cc_final: 0.8686 (tt) REVERT: C 388 TRP cc_start: 0.8039 (m-10) cc_final: 0.7825 (m-10) REVERT: D 301 MET cc_start: 0.7872 (mmm) cc_final: 0.7627 (mmp) REVERT: D 325 MET cc_start: 0.7678 (mmm) cc_final: 0.7362 (mmm) REVERT: L 210 TYR cc_start: 0.7484 (m-80) cc_final: 0.7130 (m-80) REVERT: L 388 TRP cc_start: 0.8011 (m-10) cc_final: 0.7636 (m-10) REVERT: I 325 MET cc_start: 0.7158 (mmm) cc_final: 0.6912 (mmm) REVERT: A 172 TYR cc_start: 0.7530 (t80) cc_final: 0.6925 (t80) REVERT: A 205 ASP cc_start: 0.7033 (t0) cc_final: 0.6821 (t0) REVERT: B 325 MET cc_start: 0.7987 (mmm) cc_final: 0.7464 (mmm) REVERT: B 435 TYR cc_start: 0.8062 (m-80) cc_final: 0.7489 (m-10) REVERT: K 172 TYR cc_start: 0.7745 (t80) cc_final: 0.7541 (t80) REVERT: K 178 SER cc_start: 0.7677 (OUTLIER) cc_final: 0.7440 (p) REVERT: K 205 ASP cc_start: 0.7243 (t0) cc_final: 0.6942 (t0) REVERT: K 424 ASP cc_start: 0.7875 (t70) cc_final: 0.7476 (t0) REVERT: H 94 PHE cc_start: 0.8115 (p90) cc_final: 0.7725 (p90) REVERT: H 114 LEU cc_start: 0.8904 (tp) cc_final: 0.8496 (tp) REVERT: H 398 MET cc_start: 0.8303 (mmt) cc_final: 0.8057 (mmp) outliers start: 24 outliers final: 6 residues processed: 899 average time/residue: 0.5355 time to fit residues: 766.8034 Evaluate side-chains 466 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 458 time to evaluate : 4.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain K residue 178 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 425 optimal weight: 0.9980 chunk 382 optimal weight: 1.9990 chunk 211 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 204 optimal weight: 6.9990 chunk 395 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 240 optimal weight: 7.9990 chunk 294 optimal weight: 6.9990 chunk 457 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 197 HIS E 228 ASN E 300 ASN E 329 ASN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 ASN ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 394 GLN F 406 HIS J 228 ASN J 300 ASN ** G 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 136 GLN C 197 HIS C 228 ASN C 256 GLN C 300 ASN C 329 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 101 ASN ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS L 228 ASN L 300 ASN I 133 GLN I 136 GLN I 309 HIS A 228 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN A 329 ASN A 380 ASN ** B 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 101 ASN B 337 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 GLN B 406 HIS K 197 HIS K 228 ASN K 300 ASN K 380 ASN ** H 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 136 GLN H 309 HIS Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41424 Z= 0.201 Angle : 0.598 7.784 56292 Z= 0.314 Chirality : 0.044 0.213 6156 Planarity : 0.005 0.059 7320 Dihedral : 12.052 170.871 5846 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.33 % Allowed : 12.49 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.12), residues: 5088 helix: 1.97 (0.11), residues: 2358 sheet: 0.75 (0.18), residues: 786 loop : -0.84 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 346 HIS 0.013 0.001 HIS A 88 PHE 0.021 0.002 PHE C 255 TYR 0.036 0.002 TYR E 24 ARG 0.016 0.001 ARG D 390 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 615 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 514 time to evaluate : 4.732 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: E 230 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8293 (tt) REVERT: E 398 MET cc_start: 0.7957 (tpp) cc_final: 0.7519 (mtt) REVERT: F 323 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6671 (mtp) REVERT: J 178 SER cc_start: 0.7426 (OUTLIER) cc_final: 0.7148 (p) REVERT: J 210 TYR cc_start: 0.7253 (m-80) cc_final: 0.6639 (m-80) REVERT: G 166 MET cc_start: 0.7573 (tpp) cc_final: 0.7141 (tpp) REVERT: G 302 MET cc_start: 0.7179 (mtt) cc_final: 0.6951 (mtt) REVERT: G 325 MET cc_start: 0.7459 (mmm) cc_final: 0.7057 (mmm) REVERT: G 398 MET cc_start: 0.8255 (mmt) cc_final: 0.8007 (mmp) REVERT: D 248 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7611 (tt) REVERT: L 388 TRP cc_start: 0.8119 (m-10) cc_final: 0.7685 (m-10) REVERT: A 398 MET cc_start: 0.7933 (mmm) cc_final: 0.7601 (mtt) REVERT: B 435 TYR cc_start: 0.7964 (m-80) cc_final: 0.7556 (m-10) REVERT: K 178 SER cc_start: 0.7480 (OUTLIER) cc_final: 0.7154 (p) REVERT: K 339 ARG cc_start: 0.7778 (mmp-170) cc_final: 0.7490 (mmp-170) REVERT: H 94 PHE cc_start: 0.8252 (p90) cc_final: 0.7801 (p90) REVERT: H 224 TYR cc_start: 0.7650 (OUTLIER) cc_final: 0.7308 (m-80) REVERT: H 398 MET cc_start: 0.8221 (mmt) cc_final: 0.7975 (mmp) outliers start: 101 outliers final: 43 residues processed: 594 average time/residue: 0.5093 time to fit residues: 500.3920 Evaluate side-chains 438 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 389 time to evaluate : 5.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 230 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 329 ASP Chi-restraints excluded: chain F residue 434 GLN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 434 GLN Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 178 SER Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 200 GLU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 224 TYR Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 248 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 254 optimal weight: 6.9990 chunk 142 optimal weight: 2.9990 chunk 380 optimal weight: 4.9990 chunk 311 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 458 optimal weight: 0.9990 chunk 495 optimal weight: 9.9990 chunk 408 optimal weight: 6.9990 chunk 454 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 367 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 ASN E 249 ASN E 329 ASN F 6 HIS ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 101 ASN J 406 HIS G 6 HIS G 406 HIS C 31 GLN C 101 ASN C 249 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 101 ASN L 406 HIS I 406 HIS A 101 ASN A 249 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 HIS B 294 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 406 HIS H 6 HIS H 309 HIS H 350 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 41424 Z= 0.305 Angle : 0.594 9.904 56292 Z= 0.305 Chirality : 0.044 0.225 6156 Planarity : 0.005 0.051 7320 Dihedral : 11.612 172.305 5842 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.95 % Allowed : 14.50 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.12), residues: 5088 helix: 1.68 (0.11), residues: 2352 sheet: 0.66 (0.19), residues: 786 loop : -0.76 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 346 HIS 0.012 0.001 HIS A 88 PHE 0.028 0.002 PHE A 255 TYR 0.025 0.002 TYR D 435 ARG 0.010 0.001 ARG I 284 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 403 time to evaluate : 4.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 398 MET cc_start: 0.8134 (tpp) cc_final: 0.7501 (mtt) REVERT: F 398 MET cc_start: 0.8564 (mpp) cc_final: 0.7930 (mpp) REVERT: J 210 TYR cc_start: 0.7413 (m-10) cc_final: 0.6813 (m-80) REVERT: G 302 MET cc_start: 0.7140 (mtt) cc_final: 0.6720 (mtt) REVERT: G 325 MET cc_start: 0.7505 (mmm) cc_final: 0.7098 (mmm) REVERT: G 398 MET cc_start: 0.8274 (mmt) cc_final: 0.7966 (mmp) REVERT: G 416 MET cc_start: 0.8363 (tpp) cc_final: 0.8085 (tpp) REVERT: D 248 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7748 (tt) REVERT: L 388 TRP cc_start: 0.8259 (m-10) cc_final: 0.7825 (m-10) REVERT: A 101 ASN cc_start: 0.7872 (OUTLIER) cc_final: 0.7670 (t0) REVERT: A 413 MET cc_start: 0.7992 (tpp) cc_final: 0.7645 (mpp) REVERT: B 435 TYR cc_start: 0.8054 (m-80) cc_final: 0.7838 (m-10) REVERT: K 172 TYR cc_start: 0.7882 (t80) cc_final: 0.7398 (t80) REVERT: K 339 ARG cc_start: 0.7866 (mmp-170) cc_final: 0.7662 (mmp-170) REVERT: H 94 PHE cc_start: 0.8305 (p90) cc_final: 0.7838 (p90) REVERT: H 325 MET cc_start: 0.7659 (mmm) cc_final: 0.7407 (mmm) outliers start: 128 outliers final: 74 residues processed: 506 average time/residue: 0.4768 time to fit residues: 410.4634 Evaluate side-chains 427 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 351 time to evaluate : 4.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 159 GLU Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 200 GLU Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 323 MET Chi-restraints excluded: chain F residue 378 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 434 GLN Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 113 GLU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 232 SER Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 313 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 453 optimal weight: 6.9990 chunk 344 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 218 optimal weight: 3.9990 chunk 307 optimal weight: 9.9990 chunk 460 optimal weight: 0.9980 chunk 487 optimal weight: 0.9990 chunk 240 optimal weight: 6.9990 chunk 436 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 101 ASN E 258 ASN ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 GLN L 101 ASN L 380 ASN I 294 GLN ** I 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 31 GLN A 101 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41424 Z= 0.200 Angle : 0.531 9.165 56292 Z= 0.271 Chirality : 0.042 0.233 6156 Planarity : 0.004 0.042 7320 Dihedral : 11.399 170.459 5838 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.63 % Allowed : 15.95 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.12), residues: 5088 helix: 1.71 (0.11), residues: 2322 sheet: 0.88 (0.19), residues: 810 loop : -0.72 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 346 HIS 0.009 0.001 HIS A 88 PHE 0.023 0.001 PHE F 377 TYR 0.022 0.001 TYR D 435 ARG 0.005 0.000 ARG D 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 519 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 405 time to evaluate : 5.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 398 MET cc_start: 0.8280 (tpp) cc_final: 0.7576 (mtp) REVERT: F 398 MET cc_start: 0.8681 (mpp) cc_final: 0.7937 (mpp) REVERT: J 88 HIS cc_start: 0.6626 (OUTLIER) cc_final: 0.5995 (m-70) REVERT: J 210 TYR cc_start: 0.7417 (m-10) cc_final: 0.6771 (m-80) REVERT: J 357 TYR cc_start: 0.7249 (m-80) cc_final: 0.7024 (m-10) REVERT: G 166 MET cc_start: 0.7557 (tpp) cc_final: 0.7298 (tpp) REVERT: G 302 MET cc_start: 0.7081 (mtt) cc_final: 0.6657 (mtt) REVERT: G 325 MET cc_start: 0.7489 (mmm) cc_final: 0.7086 (mmm) REVERT: G 398 MET cc_start: 0.8285 (mmt) cc_final: 0.7948 (mmp) REVERT: G 416 MET cc_start: 0.8269 (tpp) cc_final: 0.7983 (tpp) REVERT: D 75 MET cc_start: 0.8250 (mmm) cc_final: 0.7380 (mmm) REVERT: L 388 TRP cc_start: 0.8221 (m-10) cc_final: 0.7825 (m-10) REVERT: A 172 TYR cc_start: 0.7300 (OUTLIER) cc_final: 0.7088 (t80) REVERT: A 413 MET cc_start: 0.7980 (tpp) cc_final: 0.7549 (mmp) REVERT: K 172 TYR cc_start: 0.7822 (t80) cc_final: 0.7571 (t80) REVERT: H 94 PHE cc_start: 0.8289 (p90) cc_final: 0.7831 (p90) outliers start: 114 outliers final: 71 residues processed: 493 average time/residue: 0.4804 time to fit residues: 401.6362 Evaluate side-chains 426 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 353 time to evaluate : 4.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 191 VAL Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 192 HIS Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 315 VAL Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 356 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 405 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 362 optimal weight: 6.9990 chunk 201 optimal weight: 7.9990 chunk 415 optimal weight: 1.9990 chunk 336 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 437 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 31 GLN ** F 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 31 GLN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 GLN A 101 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 192 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 41424 Z= 0.208 Angle : 0.530 10.645 56292 Z= 0.268 Chirality : 0.042 0.241 6156 Planarity : 0.004 0.040 7320 Dihedral : 11.203 168.615 5838 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.95 % Allowed : 16.46 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.12), residues: 5088 helix: 1.60 (0.11), residues: 2328 sheet: 0.94 (0.19), residues: 810 loop : -0.72 (0.14), residues: 1950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP L 346 HIS 0.008 0.001 HIS A 88 PHE 0.022 0.001 PHE J 255 TYR 0.040 0.001 TYR J 24 ARG 0.006 0.000 ARG L 84 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 384 time to evaluate : 4.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 398 MET cc_start: 0.8334 (tpp) cc_final: 0.7565 (mtp) REVERT: F 398 MET cc_start: 0.8727 (mpp) cc_final: 0.7911 (mpp) REVERT: J 88 HIS cc_start: 0.6610 (OUTLIER) cc_final: 0.6103 (m-70) REVERT: J 178 SER cc_start: 0.7445 (OUTLIER) cc_final: 0.7221 (p) REVERT: J 210 TYR cc_start: 0.7421 (m-10) cc_final: 0.6777 (m-80) REVERT: G 166 MET cc_start: 0.7583 (tpp) cc_final: 0.7302 (tpp) REVERT: G 302 MET cc_start: 0.7147 (mtt) cc_final: 0.6702 (mtt) REVERT: G 325 MET cc_start: 0.7498 (mmm) cc_final: 0.7077 (mmm) REVERT: G 416 MET cc_start: 0.8266 (tpp) cc_final: 0.7992 (tpp) REVERT: D 75 MET cc_start: 0.8284 (mmm) cc_final: 0.7380 (mmm) REVERT: L 388 TRP cc_start: 0.8148 (m-10) cc_final: 0.7695 (m-10) REVERT: A 172 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6939 (t80) REVERT: A 413 MET cc_start: 0.8028 (tpp) cc_final: 0.7732 (tpp) REVERT: B 170 SER cc_start: 0.8605 (m) cc_final: 0.8241 (p) REVERT: B 398 MET cc_start: 0.8017 (mmt) cc_final: 0.7082 (mtt) REVERT: H 94 PHE cc_start: 0.8297 (p90) cc_final: 0.7831 (p90) outliers start: 128 outliers final: 86 residues processed: 477 average time/residue: 0.4737 time to fit residues: 384.4947 Evaluate side-chains 441 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 352 time to evaluate : 4.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 291 ILE Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 88 HIS Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 192 HIS Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 235 MET Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain C residue 437 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain I residue 416 MET Chi-restraints excluded: chain A residue 101 ASN Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 425 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 163 optimal weight: 3.9990 chunk 438 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 286 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 487 optimal weight: 5.9990 chunk 404 optimal weight: 8.9990 chunk 225 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 256 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 6 HIS ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 294 GLN C 101 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 HIS ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 HIS A 61 HIS ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 329 ASN A 380 ASN B 6 HIS B 8 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 434 GLN K 192 HIS H 294 GLN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 41424 Z= 0.391 Angle : 0.610 10.110 56292 Z= 0.314 Chirality : 0.045 0.217 6156 Planarity : 0.004 0.043 7320 Dihedral : 11.171 165.737 5838 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.25 % Allowed : 16.81 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.12), residues: 5088 helix: 1.29 (0.11), residues: 2346 sheet: 0.99 (0.19), residues: 762 loop : -0.92 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP L 346 HIS 0.010 0.002 HIS A 88 PHE 0.026 0.002 PHE B 377 TYR 0.023 0.002 TYR J 24 ARG 0.010 0.001 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 363 time to evaluate : 4.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 398 MET cc_start: 0.8724 (mpp) cc_final: 0.7839 (mpp) REVERT: J 178 SER cc_start: 0.7467 (OUTLIER) cc_final: 0.7034 (p) REVERT: J 203 MET cc_start: 0.6743 (OUTLIER) cc_final: 0.6438 (mtm) REVERT: G 302 MET cc_start: 0.7370 (mtt) cc_final: 0.7111 (mtt) REVERT: G 325 MET cc_start: 0.7484 (mmm) cc_final: 0.7046 (mmm) REVERT: G 416 MET cc_start: 0.8377 (tpp) cc_final: 0.8091 (tpp) REVERT: D 75 MET cc_start: 0.8313 (mmm) cc_final: 0.7436 (mmm) REVERT: D 166 MET cc_start: 0.7121 (tpp) cc_final: 0.6726 (mmm) REVERT: D 434 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.8000 (tt0) REVERT: L 254 GLU cc_start: 0.2718 (mm-30) cc_final: 0.2304 (tp30) REVERT: L 388 TRP cc_start: 0.8356 (m-10) cc_final: 0.7891 (m-10) REVERT: B 398 MET cc_start: 0.7964 (mmt) cc_final: 0.7116 (mtt) REVERT: B 425 MET cc_start: 0.8421 (mmm) cc_final: 0.8117 (tpp) REVERT: K 178 SER cc_start: 0.7638 (OUTLIER) cc_final: 0.7376 (p) REVERT: K 432 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8126 (m-80) REVERT: H 94 PHE cc_start: 0.8352 (p90) cc_final: 0.7860 (p90) outliers start: 141 outliers final: 101 residues processed: 475 average time/residue: 0.4770 time to fit residues: 383.7152 Evaluate side-chains 439 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 333 time to evaluate : 4.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 302 MET Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 150 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 203 MET Chi-restraints excluded: chain J residue 217 LEU Chi-restraints excluded: chain J residue 225 THR Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 235 MET Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 101 ASN Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 434 GLN Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 120 ASP Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 130 THR Chi-restraints excluded: chain L residue 150 THR Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 220 THR Chi-restraints excluded: chain I residue 235 MET Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain I residue 416 MET Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 378 LEU Chi-restraints excluded: chain K residue 397 LEU Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 220 THR Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 356 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 470 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 277 optimal weight: 10.0000 chunk 356 optimal weight: 2.9990 chunk 275 optimal weight: 0.5980 chunk 410 optimal weight: 1.9990 chunk 272 optimal weight: 0.2980 chunk 485 optimal weight: 7.9990 chunk 304 optimal weight: 0.0870 chunk 296 optimal weight: 0.9980 chunk 224 optimal weight: 9.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 101 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 197 HIS ** I 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 HIS ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.4015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 41424 Z= 0.156 Angle : 0.522 11.581 56292 Z= 0.265 Chirality : 0.041 0.234 6156 Planarity : 0.004 0.039 7320 Dihedral : 10.813 161.271 5838 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.40 % Allowed : 18.01 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.12), residues: 5088 helix: 1.48 (0.11), residues: 2322 sheet: 1.03 (0.19), residues: 798 loop : -0.75 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 346 HIS 0.007 0.001 HIS A 88 PHE 0.027 0.001 PHE J 255 TYR 0.030 0.001 TYR J 24 ARG 0.010 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 407 time to evaluate : 4.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 398 MET cc_start: 0.8703 (mpp) cc_final: 0.7824 (mpp) REVERT: J 178 SER cc_start: 0.7407 (OUTLIER) cc_final: 0.7035 (p) REVERT: J 203 MET cc_start: 0.6471 (OUTLIER) cc_final: 0.6182 (mtm) REVERT: G 114 LEU cc_start: 0.9261 (tp) cc_final: 0.8925 (tt) REVERT: G 257 VAL cc_start: 0.8541 (p) cc_final: 0.8312 (p) REVERT: G 302 MET cc_start: 0.7261 (mtt) cc_final: 0.6844 (mtt) REVERT: G 325 MET cc_start: 0.7405 (mmm) cc_final: 0.6976 (mmm) REVERT: G 416 MET cc_start: 0.8182 (tpp) cc_final: 0.7954 (tpp) REVERT: C 377 MET cc_start: 0.7587 (tmm) cc_final: 0.7298 (tmm) REVERT: D 75 MET cc_start: 0.8211 (mmm) cc_final: 0.7337 (mmm) REVERT: D 259 MET cc_start: 0.7169 (mmm) cc_final: 0.6754 (mtp) REVERT: D 432 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.7049 (t80) REVERT: D 434 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7817 (tt0) REVERT: L 351 PHE cc_start: 0.7449 (m-80) cc_final: 0.7193 (m-80) REVERT: L 388 TRP cc_start: 0.8261 (m-10) cc_final: 0.7873 (m-10) REVERT: B 398 MET cc_start: 0.7906 (mmt) cc_final: 0.7058 (mtt) REVERT: B 425 MET cc_start: 0.8386 (mmm) cc_final: 0.8056 (tpp) REVERT: K 172 TYR cc_start: 0.7669 (t80) cc_final: 0.7455 (t80) REVERT: K 178 SER cc_start: 0.7660 (OUTLIER) cc_final: 0.7315 (p) REVERT: K 413 MET cc_start: 0.7860 (tpp) cc_final: 0.7560 (mpp) REVERT: K 432 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.8099 (m-80) REVERT: H 94 PHE cc_start: 0.8278 (p90) cc_final: 0.7836 (p90) outliers start: 104 outliers final: 69 residues processed: 478 average time/residue: 0.4723 time to fit residues: 385.4957 Evaluate side-chains 452 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 377 time to evaluate : 4.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 203 MET Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 235 MET Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 434 GLN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 416 MET Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 172 TYR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain K residue 6 SER Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 356 CYS Chi-restraints excluded: chain H residue 425 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 300 optimal weight: 0.0870 chunk 193 optimal weight: 4.9990 chunk 290 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 308 optimal weight: 7.9990 chunk 330 optimal weight: 8.9990 chunk 240 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 381 optimal weight: 0.0370 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 18 ASN ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 258 ASN ** I 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 ASN ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 133 GLN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 349 ASN H 350 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 41424 Z= 0.144 Angle : 0.513 11.035 56292 Z= 0.258 Chirality : 0.041 0.223 6156 Planarity : 0.004 0.040 7320 Dihedral : 10.416 154.876 5838 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.08 % Allowed : 18.72 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.12), residues: 5088 helix: 1.53 (0.11), residues: 2322 sheet: 1.01 (0.19), residues: 810 loop : -0.62 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP L 346 HIS 0.006 0.001 HIS C 88 PHE 0.027 0.001 PHE J 255 TYR 0.028 0.001 TYR J 24 ARG 0.010 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 416 time to evaluate : 4.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 398 MET cc_start: 0.8711 (mpp) cc_final: 0.7797 (mpp) REVERT: J 178 SER cc_start: 0.7414 (OUTLIER) cc_final: 0.7051 (p) REVERT: J 203 MET cc_start: 0.6428 (OUTLIER) cc_final: 0.6138 (mtm) REVERT: G 114 LEU cc_start: 0.9178 (tp) cc_final: 0.8865 (tt) REVERT: G 257 VAL cc_start: 0.8505 (p) cc_final: 0.8277 (p) REVERT: G 302 MET cc_start: 0.7422 (mtt) cc_final: 0.7120 (mtt) REVERT: G 325 MET cc_start: 0.7392 (mmm) cc_final: 0.6959 (mmm) REVERT: G 416 MET cc_start: 0.8097 (tpp) cc_final: 0.7874 (tpp) REVERT: D 75 MET cc_start: 0.8138 (mmm) cc_final: 0.7616 (mmm) REVERT: D 166 MET cc_start: 0.6930 (tpp) cc_final: 0.6577 (mmm) REVERT: D 259 MET cc_start: 0.7101 (mmm) cc_final: 0.6739 (mtp) REVERT: D 432 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.7013 (t80) REVERT: D 434 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: L 351 PHE cc_start: 0.7385 (m-80) cc_final: 0.7159 (m-80) REVERT: L 388 TRP cc_start: 0.8243 (m-10) cc_final: 0.7913 (m-10) REVERT: L 425 MET cc_start: 0.7797 (tpp) cc_final: 0.7278 (tpp) REVERT: L 432 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.7420 (t80) REVERT: B 170 SER cc_start: 0.8381 (m) cc_final: 0.8119 (p) REVERT: B 398 MET cc_start: 0.7895 (mmt) cc_final: 0.7045 (mtt) REVERT: B 425 MET cc_start: 0.8409 (mmm) cc_final: 0.8097 (tpp) REVERT: K 172 TYR cc_start: 0.7654 (t80) cc_final: 0.7305 (t80) REVERT: K 178 SER cc_start: 0.7661 (OUTLIER) cc_final: 0.7301 (p) REVERT: K 413 MET cc_start: 0.7661 (tpp) cc_final: 0.7375 (mpp) REVERT: K 432 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.8224 (m-80) REVERT: H 94 PHE cc_start: 0.8331 (p90) cc_final: 0.7878 (p90) outliers start: 90 outliers final: 67 residues processed: 476 average time/residue: 0.4768 time to fit residues: 385.2001 Evaluate side-chains 452 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 378 time to evaluate : 4.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 203 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain J residue 437 VAL Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 97 SER Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 235 MET Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 199 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 291 ILE Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 434 GLN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain L residue 435 VAL Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 425 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 441 optimal weight: 5.9990 chunk 465 optimal weight: 0.0470 chunk 424 optimal weight: 6.9990 chunk 452 optimal weight: 6.9990 chunk 272 optimal weight: 0.9980 chunk 197 optimal weight: 0.0670 chunk 355 optimal weight: 10.0000 chunk 138 optimal weight: 6.9990 chunk 409 optimal weight: 3.9990 chunk 428 optimal weight: 0.5980 chunk 451 optimal weight: 0.9980 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN ** F 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 ASN ** C 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 GLN K 192 HIS K 249 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 41424 Z= 0.144 Angle : 0.521 12.759 56292 Z= 0.259 Chirality : 0.041 0.217 6156 Planarity : 0.004 0.045 7320 Dihedral : 10.087 147.092 5838 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.15 % Allowed : 18.95 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.12), residues: 5088 helix: 1.55 (0.11), residues: 2322 sheet: 1.09 (0.19), residues: 810 loop : -0.55 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A 388 HIS 0.007 0.001 HIS J 192 PHE 0.027 0.001 PHE J 255 TYR 0.044 0.001 TYR J 24 ARG 0.010 0.000 ARG D 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 420 time to evaluate : 4.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 36 MET cc_start: 0.7993 (tmm) cc_final: 0.7721 (tmm) REVERT: E 209 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8276 (mm) REVERT: E 302 MET cc_start: 0.7967 (mmm) cc_final: 0.7577 (mmm) REVERT: F 398 MET cc_start: 0.8734 (mpp) cc_final: 0.7736 (mpp) REVERT: J 178 SER cc_start: 0.7704 (OUTLIER) cc_final: 0.7385 (p) REVERT: J 203 MET cc_start: 0.6398 (OUTLIER) cc_final: 0.6090 (mtm) REVERT: G 114 LEU cc_start: 0.9160 (tp) cc_final: 0.8776 (tt) REVERT: G 257 VAL cc_start: 0.8557 (p) cc_final: 0.8355 (p) REVERT: G 302 MET cc_start: 0.7406 (mtt) cc_final: 0.7090 (mtt) REVERT: G 325 MET cc_start: 0.7404 (mmm) cc_final: 0.6974 (mmm) REVERT: G 349 ASN cc_start: 0.7914 (t0) cc_final: 0.7692 (t0) REVERT: G 416 MET cc_start: 0.8078 (tpp) cc_final: 0.7830 (tpp) REVERT: D 166 MET cc_start: 0.6981 (tpp) cc_final: 0.6699 (mmm) REVERT: D 259 MET cc_start: 0.6976 (mmm) cc_final: 0.6714 (mtp) REVERT: D 432 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7001 (t80) REVERT: D 434 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7705 (tt0) REVERT: L 388 TRP cc_start: 0.8216 (m-10) cc_final: 0.7900 (m-10) REVERT: L 425 MET cc_start: 0.7856 (tpp) cc_final: 0.7289 (tpp) REVERT: L 432 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7512 (t80) REVERT: B 398 MET cc_start: 0.7890 (mmt) cc_final: 0.7029 (mtt) REVERT: B 425 MET cc_start: 0.8502 (mmm) cc_final: 0.8168 (tpp) REVERT: K 178 SER cc_start: 0.7591 (OUTLIER) cc_final: 0.7265 (p) REVERT: K 413 MET cc_start: 0.7507 (tpp) cc_final: 0.7232 (mpp) REVERT: K 432 TYR cc_start: 0.8565 (OUTLIER) cc_final: 0.8249 (m-80) REVERT: H 94 PHE cc_start: 0.8424 (p90) cc_final: 0.7960 (p90) REVERT: H 393 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7850 (tm-30) outliers start: 93 outliers final: 67 residues processed: 483 average time/residue: 0.4810 time to fit residues: 394.5161 Evaluate side-chains 458 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 383 time to evaluate : 4.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 432 TYR Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 203 MET Chi-restraints excluded: chain J residue 248 LEU Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain G residue 37 HIS Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 235 MET Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 165 ILE Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain D residue 432 TYR Chi-restraints excluded: chain D residue 434 GLN Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 269 LEU Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 140 SER Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 248 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 425 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 297 optimal weight: 0.7980 chunk 478 optimal weight: 2.9990 chunk 292 optimal weight: 5.9990 chunk 227 optimal weight: 2.9990 chunk 332 optimal weight: 9.9990 chunk 502 optimal weight: 4.9990 chunk 462 optimal weight: 3.9990 chunk 399 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 308 optimal weight: 20.0000 chunk 245 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 ASN ** D 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 HIS ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 41424 Z= 0.297 Angle : 0.579 12.754 56292 Z= 0.293 Chirality : 0.043 0.195 6156 Planarity : 0.004 0.038 7320 Dihedral : 10.092 141.279 5838 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.03 % Allowed : 19.16 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.12), residues: 5088 helix: 1.41 (0.11), residues: 2322 sheet: 1.09 (0.19), residues: 768 loop : -0.70 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 388 HIS 0.008 0.001 HIS A 88 PHE 0.034 0.002 PHE A 255 TYR 0.035 0.001 TYR E 24 ARG 0.008 0.000 ARG L 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10176 Ramachandran restraints generated. 5088 Oldfield, 0 Emsley, 5088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 360 time to evaluate : 4.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 209 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8327 (mm) REVERT: E 302 MET cc_start: 0.8041 (mmm) cc_final: 0.7646 (mmm) REVERT: E 398 MET cc_start: 0.8017 (mmp) cc_final: 0.7672 (mmp) REVERT: F 398 MET cc_start: 0.8730 (mpp) cc_final: 0.7599 (mpp) REVERT: J 178 SER cc_start: 0.7499 (OUTLIER) cc_final: 0.7127 (p) REVERT: J 203 MET cc_start: 0.6604 (OUTLIER) cc_final: 0.6288 (mtm) REVERT: G 166 MET cc_start: 0.7596 (tpp) cc_final: 0.7229 (tpp) REVERT: G 302 MET cc_start: 0.7468 (mtt) cc_final: 0.7172 (mtt) REVERT: G 325 MET cc_start: 0.7552 (mmm) cc_final: 0.7140 (mmm) REVERT: G 416 MET cc_start: 0.8159 (tpp) cc_final: 0.7917 (tpp) REVERT: D 166 MET cc_start: 0.7161 (tpp) cc_final: 0.6797 (mmm) REVERT: D 259 MET cc_start: 0.7120 (mmm) cc_final: 0.6822 (mtp) REVERT: L 254 GLU cc_start: 0.3135 (mm-30) cc_final: 0.2643 (tp30) REVERT: L 388 TRP cc_start: 0.8336 (m-10) cc_final: 0.7988 (m-10) REVERT: L 425 MET cc_start: 0.7958 (tpp) cc_final: 0.7197 (tpp) REVERT: L 432 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.7369 (t80) REVERT: I 248 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7814 (tt) REVERT: A 36 MET cc_start: 0.7580 (tmm) cc_final: 0.7213 (tmm) REVERT: B 398 MET cc_start: 0.7918 (mmt) cc_final: 0.7093 (mtt) REVERT: B 425 MET cc_start: 0.8561 (mmm) cc_final: 0.8159 (tpp) REVERT: K 178 SER cc_start: 0.7663 (OUTLIER) cc_final: 0.7321 (p) REVERT: K 432 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8241 (m-80) REVERT: H 94 PHE cc_start: 0.8312 (p90) cc_final: 0.7833 (p90) REVERT: H 393 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7674 (tm-30) outliers start: 88 outliers final: 70 residues processed: 422 average time/residue: 0.4945 time to fit residues: 358.3052 Evaluate side-chains 426 residues out of total 4374 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 349 time to evaluate : 4.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 88 HIS Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 199 ASP Chi-restraints excluded: chain E residue 209 ILE Chi-restraints excluded: chain E residue 218 ASP Chi-restraints excluded: chain E residue 234 ILE Chi-restraints excluded: chain E residue 269 LEU Chi-restraints excluded: chain F residue 25 SER Chi-restraints excluded: chain F residue 220 THR Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain J residue 6 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 130 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 194 THR Chi-restraints excluded: chain J residue 203 MET Chi-restraints excluded: chain J residue 259 LEU Chi-restraints excluded: chain J residue 269 LEU Chi-restraints excluded: chain J residue 271 THR Chi-restraints excluded: chain J residue 391 LEU Chi-restraints excluded: chain J residue 432 TYR Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain G residue 235 MET Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 248 LEU Chi-restraints excluded: chain G residue 384 ILE Chi-restraints excluded: chain C residue 6 SER Chi-restraints excluded: chain C residue 130 THR Chi-restraints excluded: chain C residue 172 TYR Chi-restraints excluded: chain C residue 218 ASP Chi-restraints excluded: chain C residue 234 ILE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 241 CYS Chi-restraints excluded: chain L residue 4 CYS Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 191 THR Chi-restraints excluded: chain L residue 248 LEU Chi-restraints excluded: chain L residue 271 THR Chi-restraints excluded: chain L residue 275 VAL Chi-restraints excluded: chain L residue 432 TYR Chi-restraints excluded: chain I residue 86 ILE Chi-restraints excluded: chain I residue 97 SER Chi-restraints excluded: chain I residue 241 CYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain I residue 376 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 269 LEU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 241 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 130 THR Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 178 SER Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 269 LEU Chi-restraints excluded: chain K residue 275 VAL Chi-restraints excluded: chain K residue 432 TYR Chi-restraints excluded: chain K residue 435 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 235 MET Chi-restraints excluded: chain H residue 241 CYS Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 356 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 504 random chunks: chunk 317 optimal weight: 8.9990 chunk 425 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 368 optimal weight: 7.9990 chunk 59 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 400 optimal weight: 0.9990 chunk 167 optimal weight: 0.8980 chunk 411 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 chunk 73 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 350 ASN ** J 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 434 GLN ** D 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 HIS ** A 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.084994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072043 restraints weight = 88680.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074740 restraints weight = 42176.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076587 restraints weight = 25177.037| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 41424 Z= 0.158 Angle : 0.531 12.966 56292 Z= 0.264 Chirality : 0.041 0.203 6156 Planarity : 0.004 0.039 7320 Dihedral : 9.854 139.592 5838 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.78 % Allowed : 19.60 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.12), residues: 5088 helix: 1.46 (0.11), residues: 2328 sheet: 1.10 (0.19), residues: 780 loop : -0.62 (0.14), residues: 1980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 388 HIS 0.006 0.001 HIS A 88 PHE 0.026 0.001 PHE J 255 TYR 0.032 0.001 TYR J 24 ARG 0.007 0.000 ARG L 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8392.66 seconds wall clock time: 155 minutes 33.15 seconds (9333.15 seconds total)