Starting phenix.real_space_refine on Wed Apr 17 14:16:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uol_26649/04_2024/7uol_26649.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uol_26649/04_2024/7uol_26649.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/7uol_26649/04_2024/7uol_26649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uol_26649/04_2024/7uol_26649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uol_26649/04_2024/7uol_26649.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uol_26649/04_2024/7uol_26649.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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 288 5.16 5 C 28008 2.51 5 N 8016 2.21 5 O 8184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 242": "OE1" <-> "OE2" Residue "D PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ASP 365": "OD1" <-> "OD2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 446": "OE1" <-> "OE2" Residue "D ASP 447": "OD1" <-> "OD2" Residue "E GLU 242": "OE1" <-> "OE2" Residue "E PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ASP 365": "OD1" <-> "OD2" Residue "E PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 446": "OE1" <-> "OE2" Residue "E ASP 447": "OD1" <-> "OD2" Residue "F GLU 242": "OE1" <-> "OE2" Residue "F PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F ASP 365": "OD1" <-> "OD2" Residue "F PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 446": "OE1" <-> "OE2" Residue "F ASP 447": "OD1" <-> "OD2" Residue "J GLU 242": "OE1" <-> "OE2" Residue "J PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 338": "OE1" <-> "OE2" Residue "J ASP 365": "OD1" <-> "OD2" Residue "J PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 446": "OE1" <-> "OE2" Residue "J ASP 447": "OD1" <-> "OD2" Residue "K GLU 242": "OE1" <-> "OE2" Residue "K PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 338": "OE1" <-> "OE2" Residue "K ASP 365": "OD1" <-> "OD2" Residue "K PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 446": "OE1" <-> "OE2" Residue "K ASP 447": "OD1" <-> "OD2" Residue "L GLU 242": "OE1" <-> "OE2" Residue "L PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 338": "OE1" <-> "OE2" Residue "L ASP 365": "OD1" <-> "OD2" Residue "L PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 446": "OE1" <-> "OE2" Residue "L ASP 447": "OD1" <-> "OD2" Residue "M GLU 242": "OE1" <-> "OE2" Residue "M PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 338": "OE1" <-> "OE2" Residue "M ASP 365": "OD1" <-> "OD2" Residue "M PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 446": "OE1" <-> "OE2" Residue "M ASP 447": "OD1" <-> "OD2" Residue "N GLU 242": "OE1" <-> "OE2" Residue "N PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 338": "OE1" <-> "OE2" Residue "N ASP 365": "OD1" <-> "OD2" Residue "N PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 446": "OE1" <-> "OE2" Residue "N ASP 447": "OD1" <-> "OD2" Residue "O GLU 242": "OE1" <-> "OE2" Residue "O PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 338": "OE1" <-> "OE2" Residue "O ASP 365": "OD1" <-> "OD2" Residue "O PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 446": "OE1" <-> "OE2" Residue "O ASP 447": "OD1" <-> "OD2" Residue "P GLU 242": "OE1" <-> "OE2" Residue "P PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 338": "OE1" <-> "OE2" Residue "P ASP 365": "OD1" <-> "OD2" Residue "P PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 446": "OE1" <-> "OE2" Residue "P ASP 447": "OD1" <-> "OD2" Residue "Q GLU 242": "OE1" <-> "OE2" Residue "Q PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 338": "OE1" <-> "OE2" Residue "Q ASP 365": "OD1" <-> "OD2" Residue "Q PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 446": "OE1" <-> "OE2" Residue "Q ASP 447": "OD1" <-> "OD2" Residue "R GLU 242": "OE1" <-> "OE2" Residue "R PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 338": "OE1" <-> "OE2" Residue "R ASP 365": "OD1" <-> "OD2" Residue "R PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 446": "OE1" <-> "OE2" Residue "R ASP 447": "OD1" <-> "OD2" Residue "S GLU 242": "OE1" <-> "OE2" Residue "S PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 338": "OE1" <-> "OE2" Residue "S ASP 365": "OD1" <-> "OD2" Residue "S PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 446": "OE1" <-> "OE2" Residue "S ASP 447": "OD1" <-> "OD2" Residue "T GLU 242": "OE1" <-> "OE2" Residue "T PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 338": "OE1" <-> "OE2" Residue "T ASP 365": "OD1" <-> "OD2" Residue "T PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 446": "OE1" <-> "OE2" Residue "T ASP 447": "OD1" <-> "OD2" Residue "U GLU 242": "OE1" <-> "OE2" Residue "U PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 338": "OE1" <-> "OE2" Residue "U ASP 365": "OD1" <-> "OD2" Residue "U PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 446": "OE1" <-> "OE2" Residue "U ASP 447": "OD1" <-> "OD2" Residue "V GLU 242": "OE1" <-> "OE2" Residue "V PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 338": "OE1" <-> "OE2" Residue "V ASP 365": "OD1" <-> "OD2" Residue "V PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 446": "OE1" <-> "OE2" Residue "V ASP 447": "OD1" <-> "OD2" Residue "W GLU 242": "OE1" <-> "OE2" Residue "W PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 338": "OE1" <-> "OE2" Residue "W ASP 365": "OD1" <-> "OD2" Residue "W PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 446": "OE1" <-> "OE2" Residue "W ASP 447": "OD1" <-> "OD2" Residue "X GLU 242": "OE1" <-> "OE2" Residue "X PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 338": "OE1" <-> "OE2" Residue "X ASP 365": "OD1" <-> "OD2" Residue "X PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 446": "OE1" <-> "OE2" Residue "X ASP 447": "OD1" <-> "OD2" Residue "Y GLU 242": "OE1" <-> "OE2" Residue "Y PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 338": "OE1" <-> "OE2" Residue "Y ASP 365": "OD1" <-> "OD2" Residue "Y PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 446": "OE1" <-> "OE2" Residue "Y ASP 447": "OD1" <-> "OD2" Residue "Z GLU 242": "OE1" <-> "OE2" Residue "Z PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 338": "OE1" <-> "OE2" Residue "Z ASP 365": "OD1" <-> "OD2" Residue "Z PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 446": "OE1" <-> "OE2" Residue "Z ASP 447": "OD1" <-> "OD2" Residue "a GLU 242": "OE1" <-> "OE2" Residue "a PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 338": "OE1" <-> "OE2" Residue "a ASP 365": "OD1" <-> "OD2" Residue "a PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 446": "OE1" <-> "OE2" Residue "a ASP 447": "OD1" <-> "OD2" Residue "b GLU 242": "OE1" <-> "OE2" Residue "b PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 338": "OE1" <-> "OE2" Residue "b ASP 365": "OD1" <-> "OD2" Residue "b PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 446": "OE1" <-> "OE2" Residue "b ASP 447": "OD1" <-> "OD2" Residue "c GLU 242": "OE1" <-> "OE2" Residue "c PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 338": "OE1" <-> "OE2" Residue "c ASP 365": "OD1" <-> "OD2" Residue "c PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 446": "OE1" <-> "OE2" Residue "c ASP 447": "OD1" <-> "OD2" Residue "d GLU 242": "OE1" <-> "OE2" Residue "d PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 338": "OE1" <-> "OE2" Residue "d ASP 365": "OD1" <-> "OD2" Residue "d PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 446": "OE1" <-> "OE2" Residue "d ASP 447": "OD1" <-> "OD2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 44496 Number of models: 1 Model: "" Number of chains: 24 Chain: "D" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "E" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "F" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "J" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "K" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "L" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "M" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "N" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "O" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "P" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "Q" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "R" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "S" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "T" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "U" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "V" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "W" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "X" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "Y" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "Z" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "a" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "b" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "c" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Chain: "d" Number of atoms: 1854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1854 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 226} Time building chain proxies: 21.80, per 1000 atoms: 0.49 Number of scatterers: 44496 At special positions: 0 Unit cell: (148.24, 148.24, 148.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 288 16.00 O 8184 8.00 N 8016 7.00 C 28008 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: 15.67 Conformation dependent library (CDL) restraints added in 7.9 seconds 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10656 Finding SS restraints... Secondary structure from input PDB file: 240 helices and 96 sheets defined 49.2% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.07 Creating SS restraints... Processing helix chain 'D' and resid 230 through 247 Processing helix chain 'D' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG D 267 " --> pdb=" O GLU D 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP D 270 " --> pdb=" O ALA D 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA D 271 " --> pdb=" O ARG D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 297 Processing helix chain 'D' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN D 301 " --> pdb=" O GLN D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR D 339 " --> pdb=" O ASN D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS D 358 " --> pdb=" O GLU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 366 Processing helix chain 'D' and resid 377 through 380 Processing helix chain 'D' and resid 430 through 447 Processing helix chain 'D' and resid 449 through 454 Processing helix chain 'E' and resid 230 through 247 Processing helix chain 'E' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG E 267 " --> pdb=" O GLU E 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP E 270 " --> pdb=" O ALA E 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA E 271 " --> pdb=" O ARG E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 282 through 297 Processing helix chain 'E' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN E 301 " --> pdb=" O GLN E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 340 removed outlier: 3.699A pdb=" N THR E 339 " --> pdb=" O ASN E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 362 through 366 Processing helix chain 'E' and resid 377 through 380 Processing helix chain 'E' and resid 430 through 447 Processing helix chain 'E' and resid 449 through 454 Processing helix chain 'F' and resid 230 through 247 Processing helix chain 'F' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG F 267 " --> pdb=" O GLU F 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA F 271 " --> pdb=" O ARG F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 282 through 297 Processing helix chain 'F' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN F 301 " --> pdb=" O GLN F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 336 through 340 removed outlier: 3.699A pdb=" N THR F 339 " --> pdb=" O ASN F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS F 358 " --> pdb=" O GLU F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 362 through 366 Processing helix chain 'F' and resid 377 through 380 Processing helix chain 'F' and resid 430 through 447 Processing helix chain 'F' and resid 449 through 454 Processing helix chain 'J' and resid 230 through 247 Processing helix chain 'J' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG J 267 " --> pdb=" O GLU J 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP J 270 " --> pdb=" O ALA J 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA J 271 " --> pdb=" O ARG J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 282 through 297 Processing helix chain 'J' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN J 301 " --> pdb=" O GLN J 297 " (cutoff:3.500A) Processing helix chain 'J' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR J 339 " --> pdb=" O ASN J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS J 358 " --> pdb=" O GLU J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 366 Processing helix chain 'J' and resid 377 through 380 Processing helix chain 'J' and resid 430 through 447 Processing helix chain 'J' and resid 449 through 454 Processing helix chain 'K' and resid 230 through 247 Processing helix chain 'K' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG K 267 " --> pdb=" O GLU K 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP K 270 " --> pdb=" O ALA K 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA K 271 " --> pdb=" O ARG K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 297 Processing helix chain 'K' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN K 301 " --> pdb=" O GLN K 297 " (cutoff:3.500A) Processing helix chain 'K' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR K 339 " --> pdb=" O ASN K 336 " (cutoff:3.500A) Processing helix chain 'K' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS K 358 " --> pdb=" O GLU K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 366 Processing helix chain 'K' and resid 377 through 380 Processing helix chain 'K' and resid 430 through 447 Processing helix chain 'K' and resid 449 through 454 Processing helix chain 'L' and resid 230 through 247 Processing helix chain 'L' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG L 267 " --> pdb=" O GLU L 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP L 270 " --> pdb=" O ALA L 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA L 271 " --> pdb=" O ARG L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 282 through 297 Processing helix chain 'L' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN L 301 " --> pdb=" O GLN L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR L 339 " --> pdb=" O ASN L 336 " (cutoff:3.500A) Processing helix chain 'L' and resid 341 through 358 removed outlier: 3.666A pdb=" N LYS L 358 " --> pdb=" O GLU L 354 " (cutoff:3.500A) Processing helix chain 'L' and resid 362 through 366 Processing helix chain 'L' and resid 377 through 380 Processing helix chain 'L' and resid 430 through 447 Processing helix chain 'L' and resid 449 through 454 Processing helix chain 'M' and resid 230 through 247 Processing helix chain 'M' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG M 267 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP M 270 " --> pdb=" O ALA M 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA M 271 " --> pdb=" O ARG M 267 " (cutoff:3.500A) Processing helix chain 'M' and resid 282 through 297 Processing helix chain 'M' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN M 301 " --> pdb=" O GLN M 297 " (cutoff:3.500A) Processing helix chain 'M' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR M 339 " --> pdb=" O ASN M 336 " (cutoff:3.500A) Processing helix chain 'M' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS M 358 " --> pdb=" O GLU M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 362 through 366 Processing helix chain 'M' and resid 377 through 380 Processing helix chain 'M' and resid 430 through 447 Processing helix chain 'M' and resid 449 through 454 Processing helix chain 'N' and resid 230 through 247 Processing helix chain 'N' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG N 267 " --> pdb=" O GLU N 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP N 270 " --> pdb=" O ALA N 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA N 271 " --> pdb=" O ARG N 267 " (cutoff:3.500A) Processing helix chain 'N' and resid 282 through 297 Processing helix chain 'N' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN N 301 " --> pdb=" O GLN N 297 " (cutoff:3.500A) Processing helix chain 'N' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR N 339 " --> pdb=" O ASN N 336 " (cutoff:3.500A) Processing helix chain 'N' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS N 358 " --> pdb=" O GLU N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 362 through 366 Processing helix chain 'N' and resid 377 through 380 Processing helix chain 'N' and resid 430 through 447 Processing helix chain 'N' and resid 449 through 454 Processing helix chain 'O' and resid 230 through 247 Processing helix chain 'O' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG O 267 " --> pdb=" O GLU O 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP O 270 " --> pdb=" O ALA O 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA O 271 " --> pdb=" O ARG O 267 " (cutoff:3.500A) Processing helix chain 'O' and resid 282 through 297 Processing helix chain 'O' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN O 301 " --> pdb=" O GLN O 297 " (cutoff:3.500A) Processing helix chain 'O' and resid 336 through 340 removed outlier: 3.697A pdb=" N THR O 339 " --> pdb=" O ASN O 336 " (cutoff:3.500A) Processing helix chain 'O' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS O 358 " --> pdb=" O GLU O 354 " (cutoff:3.500A) Processing helix chain 'O' and resid 362 through 366 Processing helix chain 'O' and resid 377 through 380 Processing helix chain 'O' and resid 430 through 447 Processing helix chain 'O' and resid 449 through 454 Processing helix chain 'P' and resid 230 through 247 Processing helix chain 'P' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG P 267 " --> pdb=" O GLU P 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP P 270 " --> pdb=" O ALA P 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA P 271 " --> pdb=" O ARG P 267 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 297 Processing helix chain 'P' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN P 301 " --> pdb=" O GLN P 297 " (cutoff:3.500A) Processing helix chain 'P' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR P 339 " --> pdb=" O ASN P 336 " (cutoff:3.500A) Processing helix chain 'P' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS P 358 " --> pdb=" O GLU P 354 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 366 Processing helix chain 'P' and resid 377 through 380 Processing helix chain 'P' and resid 430 through 447 Processing helix chain 'P' and resid 449 through 454 Processing helix chain 'Q' and resid 230 through 247 Processing helix chain 'Q' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG Q 267 " --> pdb=" O GLU Q 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP Q 270 " --> pdb=" O ALA Q 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA Q 271 " --> pdb=" O ARG Q 267 " (cutoff:3.500A) Processing helix chain 'Q' and resid 282 through 297 Processing helix chain 'Q' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN Q 301 " --> pdb=" O GLN Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR Q 339 " --> pdb=" O ASN Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 341 through 358 removed outlier: 3.663A pdb=" N LYS Q 358 " --> pdb=" O GLU Q 354 " (cutoff:3.500A) Processing helix chain 'Q' and resid 362 through 366 Processing helix chain 'Q' and resid 377 through 380 Processing helix chain 'Q' and resid 430 through 447 Processing helix chain 'Q' and resid 449 through 454 Processing helix chain 'R' and resid 230 through 247 Processing helix chain 'R' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG R 267 " --> pdb=" O GLU R 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP R 270 " --> pdb=" O ALA R 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA R 271 " --> pdb=" O ARG R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 297 Processing helix chain 'R' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN R 301 " --> pdb=" O GLN R 297 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR R 339 " --> pdb=" O ASN R 336 " (cutoff:3.500A) Processing helix chain 'R' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS R 358 " --> pdb=" O GLU R 354 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 366 Processing helix chain 'R' and resid 377 through 380 Processing helix chain 'R' and resid 430 through 447 Processing helix chain 'R' and resid 449 through 454 Processing helix chain 'S' and resid 230 through 247 Processing helix chain 'S' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG S 267 " --> pdb=" O GLU S 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP S 270 " --> pdb=" O ALA S 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA S 271 " --> pdb=" O ARG S 267 " (cutoff:3.500A) Processing helix chain 'S' and resid 282 through 297 Processing helix chain 'S' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN S 301 " --> pdb=" O GLN S 297 " (cutoff:3.500A) Processing helix chain 'S' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR S 339 " --> pdb=" O ASN S 336 " (cutoff:3.500A) Processing helix chain 'S' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS S 358 " --> pdb=" O GLU S 354 " (cutoff:3.500A) Processing helix chain 'S' and resid 362 through 366 Processing helix chain 'S' and resid 377 through 380 Processing helix chain 'S' and resid 430 through 447 Processing helix chain 'S' and resid 449 through 454 Processing helix chain 'T' and resid 230 through 247 Processing helix chain 'T' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG T 267 " --> pdb=" O GLU T 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP T 270 " --> pdb=" O ALA T 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA T 271 " --> pdb=" O ARG T 267 " (cutoff:3.500A) Processing helix chain 'T' and resid 282 through 297 Processing helix chain 'T' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN T 301 " --> pdb=" O GLN T 297 " (cutoff:3.500A) Processing helix chain 'T' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR T 339 " --> pdb=" O ASN T 336 " (cutoff:3.500A) Processing helix chain 'T' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS T 358 " --> pdb=" O GLU T 354 " (cutoff:3.500A) Processing helix chain 'T' and resid 362 through 366 Processing helix chain 'T' and resid 377 through 380 Processing helix chain 'T' and resid 430 through 447 Processing helix chain 'T' and resid 449 through 454 Processing helix chain 'U' and resid 230 through 247 Processing helix chain 'U' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG U 267 " --> pdb=" O GLU U 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP U 270 " --> pdb=" O ALA U 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA U 271 " --> pdb=" O ARG U 267 " (cutoff:3.500A) Processing helix chain 'U' and resid 282 through 297 Processing helix chain 'U' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN U 301 " --> pdb=" O GLN U 297 " (cutoff:3.500A) Processing helix chain 'U' and resid 336 through 340 removed outlier: 3.697A pdb=" N THR U 339 " --> pdb=" O ASN U 336 " (cutoff:3.500A) Processing helix chain 'U' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS U 358 " --> pdb=" O GLU U 354 " (cutoff:3.500A) Processing helix chain 'U' and resid 362 through 366 Processing helix chain 'U' and resid 377 through 380 Processing helix chain 'U' and resid 430 through 447 Processing helix chain 'U' and resid 449 through 454 Processing helix chain 'V' and resid 230 through 247 Processing helix chain 'V' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG V 267 " --> pdb=" O GLU V 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP V 270 " --> pdb=" O ALA V 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA V 271 " --> pdb=" O ARG V 267 " (cutoff:3.500A) Processing helix chain 'V' and resid 282 through 297 Processing helix chain 'V' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN V 301 " --> pdb=" O GLN V 297 " (cutoff:3.500A) Processing helix chain 'V' and resid 336 through 340 removed outlier: 3.697A pdb=" N THR V 339 " --> pdb=" O ASN V 336 " (cutoff:3.500A) Processing helix chain 'V' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS V 358 " --> pdb=" O GLU V 354 " (cutoff:3.500A) Processing helix chain 'V' and resid 362 through 366 Processing helix chain 'V' and resid 377 through 380 Processing helix chain 'V' and resid 430 through 447 Processing helix chain 'V' and resid 449 through 454 Processing helix chain 'W' and resid 230 through 247 Processing helix chain 'W' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG W 267 " --> pdb=" O GLU W 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP W 270 " --> pdb=" O ALA W 266 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ALA W 271 " --> pdb=" O ARG W 267 " (cutoff:3.500A) Processing helix chain 'W' and resid 282 through 297 Processing helix chain 'W' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN W 301 " --> pdb=" O GLN W 297 " (cutoff:3.500A) Processing helix chain 'W' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR W 339 " --> pdb=" O ASN W 336 " (cutoff:3.500A) Processing helix chain 'W' and resid 341 through 358 removed outlier: 3.663A pdb=" N LYS W 358 " --> pdb=" O GLU W 354 " (cutoff:3.500A) Processing helix chain 'W' and resid 362 through 366 Processing helix chain 'W' and resid 377 through 380 Processing helix chain 'W' and resid 430 through 447 Processing helix chain 'W' and resid 449 through 454 Processing helix chain 'X' and resid 230 through 247 Processing helix chain 'X' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG X 267 " --> pdb=" O GLU X 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP X 270 " --> pdb=" O ALA X 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA X 271 " --> pdb=" O ARG X 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 282 through 297 Processing helix chain 'X' and resid 297 through 302 removed outlier: 3.894A pdb=" N ASN X 301 " --> pdb=" O GLN X 297 " (cutoff:3.500A) Processing helix chain 'X' and resid 336 through 340 removed outlier: 3.697A pdb=" N THR X 339 " --> pdb=" O ASN X 336 " (cutoff:3.500A) Processing helix chain 'X' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS X 358 " --> pdb=" O GLU X 354 " (cutoff:3.500A) Processing helix chain 'X' and resid 362 through 366 Processing helix chain 'X' and resid 377 through 380 Processing helix chain 'X' and resid 430 through 447 Processing helix chain 'X' and resid 449 through 454 Processing helix chain 'Y' and resid 230 through 247 Processing helix chain 'Y' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG Y 267 " --> pdb=" O GLU Y 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP Y 270 " --> pdb=" O ALA Y 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA Y 271 " --> pdb=" O ARG Y 267 " (cutoff:3.500A) Processing helix chain 'Y' and resid 282 through 297 Processing helix chain 'Y' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN Y 301 " --> pdb=" O GLN Y 297 " (cutoff:3.500A) Processing helix chain 'Y' and resid 336 through 340 removed outlier: 3.699A pdb=" N THR Y 339 " --> pdb=" O ASN Y 336 " (cutoff:3.500A) Processing helix chain 'Y' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS Y 358 " --> pdb=" O GLU Y 354 " (cutoff:3.500A) Processing helix chain 'Y' and resid 362 through 366 Processing helix chain 'Y' and resid 377 through 380 Processing helix chain 'Y' and resid 430 through 447 Processing helix chain 'Y' and resid 449 through 454 Processing helix chain 'Z' and resid 230 through 247 Processing helix chain 'Z' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP Z 270 " --> pdb=" O ALA Z 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA Z 271 " --> pdb=" O ARG Z 267 " (cutoff:3.500A) Processing helix chain 'Z' and resid 282 through 297 Processing helix chain 'Z' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN Z 301 " --> pdb=" O GLN Z 297 " (cutoff:3.500A) Processing helix chain 'Z' and resid 336 through 340 removed outlier: 3.699A pdb=" N THR Z 339 " --> pdb=" O ASN Z 336 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS Z 358 " --> pdb=" O GLU Z 354 " (cutoff:3.500A) Processing helix chain 'Z' and resid 362 through 366 Processing helix chain 'Z' and resid 377 through 380 Processing helix chain 'Z' and resid 430 through 447 Processing helix chain 'Z' and resid 449 through 454 Processing helix chain 'a' and resid 230 through 247 Processing helix chain 'a' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG a 267 " --> pdb=" O GLU a 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP a 270 " --> pdb=" O ALA a 266 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N ALA a 271 " --> pdb=" O ARG a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 282 through 297 Processing helix chain 'a' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN a 301 " --> pdb=" O GLN a 297 " (cutoff:3.500A) Processing helix chain 'a' and resid 336 through 340 removed outlier: 3.699A pdb=" N THR a 339 " --> pdb=" O ASN a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 341 through 358 removed outlier: 3.664A pdb=" N LYS a 358 " --> pdb=" O GLU a 354 " (cutoff:3.500A) Processing helix chain 'a' and resid 362 through 366 Processing helix chain 'a' and resid 377 through 380 Processing helix chain 'a' and resid 430 through 447 Processing helix chain 'a' and resid 449 through 454 Processing helix chain 'b' and resid 230 through 247 Processing helix chain 'b' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG b 267 " --> pdb=" O GLU b 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP b 270 " --> pdb=" O ALA b 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA b 271 " --> pdb=" O ARG b 267 " (cutoff:3.500A) Processing helix chain 'b' and resid 282 through 297 Processing helix chain 'b' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN b 301 " --> pdb=" O GLN b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR b 339 " --> pdb=" O ASN b 336 " (cutoff:3.500A) Processing helix chain 'b' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS b 358 " --> pdb=" O GLU b 354 " (cutoff:3.500A) Processing helix chain 'b' and resid 362 through 366 Processing helix chain 'b' and resid 377 through 380 Processing helix chain 'b' and resid 430 through 447 Processing helix chain 'b' and resid 449 through 454 Processing helix chain 'c' and resid 230 through 247 Processing helix chain 'c' and resid 258 through 277 removed outlier: 3.798A pdb=" N ARG c 267 " --> pdb=" O GLU c 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP c 270 " --> pdb=" O ALA c 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA c 271 " --> pdb=" O ARG c 267 " (cutoff:3.500A) Processing helix chain 'c' and resid 282 through 297 Processing helix chain 'c' and resid 297 through 302 removed outlier: 3.895A pdb=" N ASN c 301 " --> pdb=" O GLN c 297 " (cutoff:3.500A) Processing helix chain 'c' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR c 339 " --> pdb=" O ASN c 336 " (cutoff:3.500A) Processing helix chain 'c' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS c 358 " --> pdb=" O GLU c 354 " (cutoff:3.500A) Processing helix chain 'c' and resid 362 through 366 Processing helix chain 'c' and resid 377 through 380 Processing helix chain 'c' and resid 430 through 447 Processing helix chain 'c' and resid 449 through 454 Processing helix chain 'd' and resid 230 through 247 Processing helix chain 'd' and resid 258 through 277 removed outlier: 3.799A pdb=" N ARG d 267 " --> pdb=" O GLU d 263 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ASP d 270 " --> pdb=" O ALA d 266 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA d 271 " --> pdb=" O ARG d 267 " (cutoff:3.500A) Processing helix chain 'd' and resid 282 through 297 Processing helix chain 'd' and resid 297 through 302 removed outlier: 3.896A pdb=" N ASN d 301 " --> pdb=" O GLN d 297 " (cutoff:3.500A) Processing helix chain 'd' and resid 336 through 340 removed outlier: 3.698A pdb=" N THR d 339 " --> pdb=" O ASN d 336 " (cutoff:3.500A) Processing helix chain 'd' and resid 341 through 358 removed outlier: 3.665A pdb=" N LYS d 358 " --> pdb=" O GLU d 354 " (cutoff:3.500A) Processing helix chain 'd' and resid 362 through 366 Processing helix chain 'd' and resid 377 through 380 Processing helix chain 'd' and resid 430 through 447 Processing helix chain 'd' and resid 449 through 454 Processing sheet with id=AA1, first strand: chain 'D' and resid 226 through 228 Processing sheet with id=AA2, first strand: chain 'D' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR D 372 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR D 372 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N PHE F 383 " --> pdb=" O PHE D 253 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 303 through 305 Processing sheet with id=AA5, first strand: chain 'D' and resid 323 through 325 Processing sheet with id=AA6, first strand: chain 'D' and resid 383 through 384 removed outlier: 3.926A pdb=" N PHE D 383 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR E 372 " --> pdb=" O ALA E 394 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 383 through 384 removed outlier: 3.926A pdb=" N PHE D 383 " --> pdb=" O PHE E 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 226 through 228 Processing sheet with id=AA9, first strand: chain 'E' and resid 323 through 325 Processing sheet with id=AB1, first strand: chain 'E' and resid 383 through 384 removed outlier: 3.937A pdb=" N PHE E 383 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR F 372 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 383 through 384 removed outlier: 3.937A pdb=" N PHE E 383 " --> pdb=" O PHE F 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 323 through 325 Processing sheet with id=AB4, first strand: chain 'J' and resid 226 through 228 Processing sheet with id=AB5, first strand: chain 'J' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR J 372 " --> pdb=" O ALA J 394 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR J 372 " --> pdb=" O ALA J 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE K 383 " --> pdb=" O PHE J 253 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 303 through 305 Processing sheet with id=AB8, first strand: chain 'J' and resid 323 through 325 Processing sheet with id=AB9, first strand: chain 'J' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE J 383 " --> pdb=" O PHE L 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR L 372 " --> pdb=" O ALA L 394 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE J 383 " --> pdb=" O PHE L 253 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR K 372 " --> pdb=" O ALA K 394 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR K 372 " --> pdb=" O ALA K 394 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE L 383 " --> pdb=" O PHE K 253 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 303 through 305 Processing sheet with id=AC5, first strand: chain 'K' and resid 323 through 325 Processing sheet with id=AC6, first strand: chain 'L' and resid 323 through 325 Processing sheet with id=AC7, first strand: chain 'M' and resid 226 through 228 Processing sheet with id=AC8, first strand: chain 'M' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR M 372 " --> pdb=" O ALA M 394 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR M 372 " --> pdb=" O ALA M 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE N 383 " --> pdb=" O PHE M 253 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 303 through 305 Processing sheet with id=AD2, first strand: chain 'M' and resid 323 through 325 Processing sheet with id=AD3, first strand: chain 'M' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE M 383 " --> pdb=" O PHE O 253 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR O 372 " --> pdb=" O ALA O 394 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE M 383 " --> pdb=" O PHE O 253 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR N 372 " --> pdb=" O ALA N 394 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR N 372 " --> pdb=" O ALA N 394 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE O 383 " --> pdb=" O PHE N 253 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 303 through 305 Processing sheet with id=AD8, first strand: chain 'N' and resid 323 through 325 Processing sheet with id=AD9, first strand: chain 'O' and resid 323 through 325 Processing sheet with id=AE1, first strand: chain 'P' and resid 226 through 228 Processing sheet with id=AE2, first strand: chain 'P' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR P 372 " --> pdb=" O ALA P 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'P' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR P 372 " --> pdb=" O ALA P 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE Q 383 " --> pdb=" O PHE P 253 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'P' and resid 303 through 305 Processing sheet with id=AE5, first strand: chain 'P' and resid 323 through 325 Processing sheet with id=AE6, first strand: chain 'P' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE P 383 " --> pdb=" O PHE R 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR R 372 " --> pdb=" O ALA R 394 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE P 383 " --> pdb=" O PHE R 253 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR Q 372 " --> pdb=" O ALA Q 394 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR Q 372 " --> pdb=" O ALA Q 394 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE R 383 " --> pdb=" O PHE Q 253 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 303 through 305 Processing sheet with id=AF2, first strand: chain 'Q' and resid 323 through 325 Processing sheet with id=AF3, first strand: chain 'R' and resid 323 through 325 Processing sheet with id=AF4, first strand: chain 'S' and resid 226 through 228 Processing sheet with id=AF5, first strand: chain 'S' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR S 372 " --> pdb=" O ALA S 394 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'S' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR S 372 " --> pdb=" O ALA S 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE T 383 " --> pdb=" O PHE S 253 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'S' and resid 303 through 305 Processing sheet with id=AF8, first strand: chain 'S' and resid 323 through 325 Processing sheet with id=AF9, first strand: chain 'S' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE S 383 " --> pdb=" O PHE U 253 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N THR U 372 " --> pdb=" O ALA U 394 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE S 383 " --> pdb=" O PHE U 253 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'T' and resid 333 through 334 removed outlier: 4.208A pdb=" N THR T 372 " --> pdb=" O ALA T 394 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'T' and resid 333 through 334 removed outlier: 4.208A pdb=" N THR T 372 " --> pdb=" O ALA T 394 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE U 383 " --> pdb=" O PHE T 253 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'T' and resid 303 through 305 Processing sheet with id=AG5, first strand: chain 'T' and resid 323 through 325 Processing sheet with id=AG6, first strand: chain 'U' and resid 323 through 325 Processing sheet with id=AG7, first strand: chain 'V' and resid 226 through 228 Processing sheet with id=AG8, first strand: chain 'V' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR V 372 " --> pdb=" O ALA V 394 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR V 372 " --> pdb=" O ALA V 394 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE W 383 " --> pdb=" O PHE V 253 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'V' and resid 303 through 305 Processing sheet with id=AH2, first strand: chain 'V' and resid 323 through 325 Processing sheet with id=AH3, first strand: chain 'V' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE V 383 " --> pdb=" O PHE X 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR X 372 " --> pdb=" O ALA X 394 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'V' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE V 383 " --> pdb=" O PHE X 253 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'W' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR W 372 " --> pdb=" O ALA W 394 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR W 372 " --> pdb=" O ALA W 394 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE X 383 " --> pdb=" O PHE W 253 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'W' and resid 303 through 305 Processing sheet with id=AH8, first strand: chain 'W' and resid 323 through 325 Processing sheet with id=AH9, first strand: chain 'X' and resid 323 through 325 Processing sheet with id=AI1, first strand: chain 'Y' and resid 226 through 228 Processing sheet with id=AI2, first strand: chain 'Y' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR Y 372 " --> pdb=" O ALA Y 394 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'Y' and resid 333 through 334 removed outlier: 4.206A pdb=" N THR Y 372 " --> pdb=" O ALA Y 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE Z 383 " --> pdb=" O PHE Y 253 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Y' and resid 303 through 305 Processing sheet with id=AI5, first strand: chain 'Y' and resid 323 through 325 Processing sheet with id=AI6, first strand: chain 'Y' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE Y 383 " --> pdb=" O PHE a 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR a 372 " --> pdb=" O ALA a 394 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Y' and resid 383 through 384 removed outlier: 3.952A pdb=" N PHE Y 383 " --> pdb=" O PHE a 253 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Z' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR Z 372 " --> pdb=" O ALA Z 394 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Z' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR Z 372 " --> pdb=" O ALA Z 394 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N PHE a 383 " --> pdb=" O PHE Z 253 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Z' and resid 303 through 305 Processing sheet with id=AJ2, first strand: chain 'Z' and resid 323 through 325 Processing sheet with id=AJ3, first strand: chain 'a' and resid 323 through 325 Processing sheet with id=AJ4, first strand: chain 'b' and resid 226 through 228 Processing sheet with id=AJ5, first strand: chain 'b' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR b 372 " --> pdb=" O ALA b 394 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'b' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR b 372 " --> pdb=" O ALA b 394 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N PHE c 383 " --> pdb=" O PHE b 253 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'b' and resid 303 through 305 Processing sheet with id=AJ8, first strand: chain 'b' and resid 323 through 325 Processing sheet with id=AJ9, first strand: chain 'b' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE b 383 " --> pdb=" O PHE d 253 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR d 372 " --> pdb=" O ALA d 394 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'b' and resid 383 through 384 removed outlier: 3.953A pdb=" N PHE b 383 " --> pdb=" O PHE d 253 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'c' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR c 372 " --> pdb=" O ALA c 394 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'c' and resid 333 through 334 removed outlier: 4.207A pdb=" N THR c 372 " --> pdb=" O ALA c 394 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE d 383 " --> pdb=" O PHE c 253 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'c' and resid 303 through 305 Processing sheet with id=AK5, first strand: chain 'c' and resid 323 through 325 Processing sheet with id=AK6, first strand: chain 'd' and resid 323 through 325 2910 hydrogen bonds defined for protein. 7893 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: 23.21 Time building geometry restraints manager: 17.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 15216 1.34 - 1.46: 8723 1.46 - 1.58: 20653 1.58 - 1.70: 0 1.70 - 1.82: 552 Bond restraints: 45144 Sorted by residual: bond pdb=" N GLY U 220 " pdb=" CA GLY U 220 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.23e+00 bond pdb=" N GLY X 220 " pdb=" CA GLY X 220 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.13e+00 bond pdb=" N GLY L 220 " pdb=" CA GLY L 220 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.10e+00 bond pdb=" N GLY V 220 " pdb=" CA GLY V 220 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.07e+00 bond pdb=" N GLY J 220 " pdb=" CA GLY J 220 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.07e+00 ... (remaining 45139 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.47: 1176 106.47 - 112.76: 24221 112.76 - 119.04: 12246 119.04 - 125.33: 22909 125.33 - 131.62: 336 Bond angle restraints: 60888 Sorted by residual: angle pdb=" N ASN M 359 " pdb=" CA ASN M 359 " pdb=" C ASN M 359 " ideal model delta sigma weight residual 113.01 117.12 -4.11 1.20e+00 6.94e-01 1.17e+01 angle pdb=" N ASN S 359 " pdb=" CA ASN S 359 " pdb=" C ASN S 359 " ideal model delta sigma weight residual 113.01 117.11 -4.10 1.20e+00 6.94e-01 1.17e+01 angle pdb=" N ASN V 359 " pdb=" CA ASN V 359 " pdb=" C ASN V 359 " ideal model delta sigma weight residual 113.01 117.08 -4.07 1.20e+00 6.94e-01 1.15e+01 angle pdb=" N ASN T 359 " pdb=" CA ASN T 359 " pdb=" C ASN T 359 " ideal model delta sigma weight residual 113.01 117.08 -4.07 1.20e+00 6.94e-01 1.15e+01 angle pdb=" N ASN D 359 " pdb=" CA ASN D 359 " pdb=" C ASN D 359 " ideal model delta sigma weight residual 113.01 117.08 -4.07 1.20e+00 6.94e-01 1.15e+01 ... (remaining 60883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 24912 15.99 - 31.99: 2328 31.99 - 47.98: 576 47.98 - 63.97: 144 63.97 - 79.97: 48 Dihedral angle restraints: 28008 sinusoidal: 11592 harmonic: 16416 Sorted by residual: dihedral pdb=" CA ASN R 389 " pdb=" C ASN R 389 " pdb=" N PRO R 390 " pdb=" CA PRO R 390 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASN O 389 " pdb=" C ASN O 389 " pdb=" N PRO O 390 " pdb=" CA PRO O 390 " ideal model delta harmonic sigma weight residual -180.00 -158.07 -21.93 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA ASN X 389 " pdb=" C ASN X 389 " pdb=" N PRO X 390 " pdb=" CA PRO X 390 " ideal model delta harmonic sigma weight residual -180.00 -158.08 -21.92 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 28005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 4043 0.025 - 0.051: 1740 0.051 - 0.076: 519 0.076 - 0.101: 230 0.101 - 0.126: 500 Chirality restraints: 7032 Sorted by residual: chirality pdb=" CA ILE R 408 " pdb=" N ILE R 408 " pdb=" C ILE R 408 " pdb=" CB ILE R 408 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE d 408 " pdb=" N ILE d 408 " pdb=" C ILE d 408 " pdb=" CB ILE d 408 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA ILE U 408 " pdb=" N ILE U 408 " pdb=" C ILE U 408 " pdb=" CB ILE U 408 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 7029 not shown) Planarity restraints: 7944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS a 358 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.67e+00 pdb=" C LYS a 358 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS a 358 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN a 359 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 358 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C LYS E 358 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS E 358 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN E 359 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 358 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C LYS R 358 " -0.028 2.00e-02 2.50e+03 pdb=" O LYS R 358 " 0.011 2.00e-02 2.50e+03 pdb=" N ASN R 359 " 0.009 2.00e-02 2.50e+03 ... (remaining 7941 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 16288 2.88 - 3.39: 43373 3.39 - 3.89: 69534 3.89 - 4.40: 76849 4.40 - 4.90: 136016 Nonbonded interactions: 342060 Sorted by model distance: nonbonded pdb=" OE2 GLU a 242 " pdb=" OG1 THR a 246 " model vdw 2.380 2.440 nonbonded pdb=" OE2 GLU c 242 " pdb=" OG1 THR c 246 " model vdw 2.380 2.440 nonbonded pdb=" OE2 GLU T 242 " pdb=" OG1 THR T 246 " model vdw 2.380 2.440 nonbonded pdb=" OE2 GLU K 242 " pdb=" OG1 THR K 246 " model vdw 2.380 2.440 nonbonded pdb=" OE2 GLU b 242 " pdb=" OG1 THR b 246 " model vdw 2.380 2.440 ... (remaining 342055 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 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } 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: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 13.950 Check model and map are aligned: 0.690 Set scattering table: 0.370 Process input model: 115.260 Find NCS groups from input model: 3.010 Set up NCS constraints: 0.400 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 140.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45144 Z= 0.207 Angle : 0.579 6.668 60888 Z= 0.343 Chirality : 0.042 0.126 7032 Planarity : 0.003 0.023 7944 Dihedral : 14.152 79.967 17352 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.50 % Allowed : 7.42 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.11), residues: 5616 helix: 1.88 (0.11), residues: 2256 sheet: 0.08 (0.18), residues: 864 loop : -0.98 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS c 225 PHE 0.010 0.001 PHE b 437 TYR 0.006 0.001 TYR V 419 ARG 0.003 0.000 ARG S 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 4800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 569 time to evaluate : 5.045 Fit side-chains REVERT: Q 238 GLN cc_start: 0.7798 (tp40) cc_final: 0.7595 (tm-30) outliers start: 24 outliers final: 24 residues processed: 593 average time/residue: 0.5667 time to fit residues: 571.6111 Evaluate side-chains 433 residues out of total 4800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 409 time to evaluate : 5.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 466 optimal weight: 0.8980 chunk 418 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 282 optimal weight: 0.5980 chunk 223 optimal weight: 0.6980 chunk 432 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 chunk 263 optimal weight: 0.0870 chunk 322 optimal weight: 0.9990 chunk 501 optimal weight: 0.0970 overall best weight: 0.4556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45144 Z= 0.192 Angle : 0.497 4.910 60888 Z= 0.278 Chirality : 0.042 0.140 7032 Planarity : 0.004 0.031 7944 Dihedral : 5.530 38.709 6288 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.21 % Allowed : 10.33 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.11), residues: 5616 helix: 2.32 (0.11), residues: 2304 sheet: 0.16 (0.16), residues: 912 loop : -0.57 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 225 PHE 0.014 0.002 PHE P 437 TYR 0.005 0.001 TYR a 313 ARG 0.003 0.000 ARG J 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 4800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 452 time to evaluate : 5.157 Fit side-chains REVERT: F 309 LYS cc_start: 0.7792 (mppt) cc_final: 0.7470 (tppt) REVERT: F 373 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8894 (mt) REVERT: K 373 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8876 (mt) REVERT: L 309 LYS cc_start: 0.7698 (mppt) cc_final: 0.7418 (tppt) REVERT: O 309 LYS cc_start: 0.7678 (mppt) cc_final: 0.7430 (tppt) REVERT: P 373 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8935 (mt) REVERT: Q 238 GLN cc_start: 0.7891 (tp40) cc_final: 0.7586 (tm-30) REVERT: R 309 LYS cc_start: 0.7795 (mppt) cc_final: 0.7491 (tppt) REVERT: S 309 LYS cc_start: 0.7762 (mppt) cc_final: 0.7549 (tppt) REVERT: S 373 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8933 (mt) REVERT: T 373 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8864 (mt) REVERT: U 309 LYS cc_start: 0.7687 (mppt) cc_final: 0.7470 (tppt) REVERT: W 309 LYS cc_start: 0.7701 (mppt) cc_final: 0.7467 (tppt) REVERT: W 373 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8868 (mt) REVERT: a 309 LYS cc_start: 0.7697 (mppt) cc_final: 0.7376 (tppt) REVERT: b 309 LYS cc_start: 0.7755 (mppt) cc_final: 0.7485 (tppt) REVERT: c 229 MET cc_start: 0.8312 (OUTLIER) cc_final: 0.8025 (mtt) REVERT: c 373 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8900 (mt) REVERT: d 309 LYS cc_start: 0.7683 (mppt) cc_final: 0.7482 (tppt) outliers start: 106 outliers final: 24 residues processed: 535 average time/residue: 0.5914 time to fit residues: 512.0614 Evaluate side-chains 398 residues out of total 4800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 366 time to evaluate : 5.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain K residue 373 ILE Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain P residue 373 ILE Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain S residue 373 ILE Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain T residue 373 ILE Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain W residue 373 ILE Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 229 MET Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain c residue 373 ILE Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 278 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 417 optimal weight: 2.9990 chunk 341 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 502 optimal weight: 0.9990 chunk 542 optimal weight: 0.0070 chunk 447 optimal weight: 0.2980 chunk 497 optimal weight: 1.9990 chunk 171 optimal weight: 0.7980 chunk 402 optimal weight: 0.0970 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45144 Z= 0.179 Angle : 0.475 6.856 60888 Z= 0.258 Chirality : 0.042 0.137 7032 Planarity : 0.004 0.037 7944 Dihedral : 5.294 37.060 6288 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.58 % Allowed : 12.50 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.11), residues: 5616 helix: 2.59 (0.11), residues: 2304 sheet: -0.00 (0.19), residues: 768 loop : -0.51 (0.12), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS c 399 PHE 0.016 0.002 PHE P 437 TYR 0.005 0.001 TYR W 316 ARG 0.003 0.000 ARG W 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 4800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 528 time to evaluate : 5.135 Fit side-chains revert: symmetry clash REVERT: D 283 MET cc_start: 0.9025 (tpp) cc_final: 0.8581 (tpp) REVERT: D 305 ASP cc_start: 0.7465 (t0) cc_final: 0.7166 (t0) REVERT: E 283 MET cc_start: 0.9030 (tpp) cc_final: 0.8575 (tpp) REVERT: F 283 MET cc_start: 0.9014 (tpp) cc_final: 0.8506 (tpp) REVERT: F 309 LYS cc_start: 0.7883 (mppt) cc_final: 0.7651 (tppt) REVERT: J 283 MET cc_start: 0.9031 (tpp) cc_final: 0.8574 (tpp) REVERT: J 305 ASP cc_start: 0.7467 (t0) cc_final: 0.7164 (t0) REVERT: K 283 MET cc_start: 0.9078 (tpp) cc_final: 0.8522 (tpp) REVERT: K 305 ASP cc_start: 0.7535 (t0) cc_final: 0.7210 (t0) REVERT: K 321 VAL cc_start: 0.9215 (p) cc_final: 0.9014 (m) REVERT: L 283 MET cc_start: 0.9069 (tpp) cc_final: 0.8499 (tpp) REVERT: L 309 LYS cc_start: 0.7862 (mppt) cc_final: 0.75------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 496 optimal weight: 0.4980 chunk 377 optimal weight: 2.9990 chunk 260 optimal weight: 2.9990 chunk 55 optimal weight: 0.5980 chunk 239 optimal weight: 2.9990 chunk 337 optimal weight: 0.6980 chunk 503 optimal weight: 2.9990 chunk 533 optimal weight: 0.6980 chunk 263 optimal weight: 0.5980 chunk 477 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 45144 Z= 0.205 Angle : 0.493 7.407 60888 Z= 0.262 Chirality : 0.042 0.139 7032 Planarity : 0.004 0.040 7944 Dihedral : 4.625 20.214 6240 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.17 % Allowed : 13.25 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.11), residues: 5616 helix: 2.79 (0.11), residues: 2280 sheet: -0.06 (0.18), residues: 768 loop : -0.61 (0.12), residues: 2568 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS L 399 PHE 0.014 0.002 PHE U 437 TYR 0.006 0.001 TYR W 419 ARG 0.003 0.000 ARG V 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 4800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 462 time to evaluate : 4.981 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: D 283 MET cc_start: 0.9065 (tpp) cc_final: 0.8527 (tpp) REVERT: D 305 ASP cc_start: 0.7522 (t0) cc_final: 0.6727 (p0) REVERT: E 283 MET cc_start: 0.9043 (tpp) cc_final: 0.8524 (tpp) REVERT: F 283 MET cc_start: 0.9015 (tpp) cc_final: 0.8513 (tpp) REVERT: J 283 MET cc_start: 0.9052 (tpp) cc_final: 0.8563 (tpp) REVERT: J 305 ASP cc_start: 0.7520 (t0) cc_final: 0.6730 (p0) REVERT: K 283 MET cc_start: 0.9030 (tpp) cc_final: 0.8521 (tpp) REVERT: K 305 ASP cc_start: 0.7513 (t0) cc_final: 0.6738 (p0) REVERT: L 283 MET cc_start: 0.9034 (tpp) cc_final: 0.8500 (tpp) REVERT: M 283 MET cc_start: 0.9041 (tpp) cc_final: 0.8544 (tpp) REVERT: M 305 ASP cc_start: 0.7521 (t0) cc_final: 0.6730 (p0) REVERT: N 283 MET cc_start: 0.9041 (tpp) cc_final: 0.8537 (tpp) REVERT: N 305 ASP cc_start: 0.7507 (t0) cc_final: 0.6728 (p0) REVERT: O 283 MET cc_start: 0.9048 (tpp) cc_final: 0.8538 (tpp) REVERT: P 283 MET cc_start: 0.9017 (tpp) cc_final: 0.8520 (tpp) REVERT: P 305 ASP cc_start: 0.7501 (t0) cc_final: 0.6717 (p0) REVERT: Q 238 GLN cc_start: 0.7855 (tp40) cc_final: 0.7484 (tm-30) REVERT: Q 283 MET cc_start: 0.9050 (tpp) cc_final: 0.8538 (tpp) REVERT: Q 305 ASP cc_start: 0.7493 (t0) cc_final: 0.6724 (p0) REVERT: R 283 MET cc_start: 0.9026 (tpp) cc_final: 0.8525 (tpp) REVERT: S 283 MET cc_start: 0.8999 (tpp) cc_final: 0.8496 (tpp) REVERT: S 309 LYS cc_start: 0.8129 (mppt) cc_final: 0.7843 (tppt) REVERT: T 283 MET cc_start: 0.9026 (tpp) cc_final: 0.8490 (tpp) REVERT: T 305 ASP cc_start: 0.7512 (t0) cc_final: 0.6732 (p0) REVERT: U 283 MET cc_start: 0.9034 (tpp) cc_final: 0.8537 (tpp) REVERT: V 283 MET cc_start: 0.9038 (tpp) cc_final: 0.8546 (tpp) REVERT: W 283 MET cc_start: 0.9039 (tpp) cc_final: 0------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 444 optimal weight: 2.9990 chunk 302 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 397 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 455 optimal weight: 2.9990 chunk 368 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 272 optimal weight: 3.9990 chunk 478 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 45144 Z= 0.340 Angle : 0.548 5.716 60888 Z= 0.292 Chirality : 0.044 0.148 7032 Planarity : 0.004 0.043 7944 Dihedral : 4.840 19.987 6240 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.88 % Allowed : 14.27 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.11), residues: 5616 helix: 2.58 (0.11), residues: 2280 sheet: -0.37 (0.19), residues: 744 loop : -0.72 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS Z 399 PHE 0.012 0.002 PHE Z 437 TYR 0.012 0.002 TYR D 419 ARG 0.003 0.000 ARG D 235 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 437 time to evaluate : 4.793 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 283 MET cc_start: 0.9045 (tpp) cc_final: 0.8523 (tpp) REVERT: D 305 ASP cc_start: 0.7462 (t0) cc_final: 0.6694 (p0) REVERT: J 305 ASP cc_start: 0.7428 (t0) cc_final: 0.7126 (t0) REVERT: K 305 ASP cc_start: 0.7416 (t0) cc_final: 0.7107 (t0) REVERT: M 305 ASP cc_start: 0.7433 (t0) cc_final: 0.7116 (t0) REVERT: N 283 MET cc_start: 0.9036 (tpp) cc_final: 0.8538 (tpp) REVERT: N 305 ASP cc_start: 0.7408 (t0) cc_final: 0.7112 (t0) REVERT: P 305 ASP cc_start: 0.7368 (t0) cc_final: 0.6679 (p0) REVERT: Q 238 GLN cc_start: 0.7858 (tp40) cc_final: 0.7491 (tm-30) REVERT: Q 283 MET cc_start: 0.9044 (tpp) cc_final: 0.8518 (tpp) REVERT: Q 305 ASP cc_start: 0.7375 (t0) cc_final: 0.7073 (t0) REVERT: S 283 MET cc_start: 0.9015 (tpp) cc_final: 0.8541 (tpp) REVERT: T 305 ASP cc_start: 0.7424 (t0) cc_final: 0.7104 (t0) REVERT: Y 305 ASP cc_start: 0.7434 (t0) cc_final: 0.7122 (t0) REVERT: Z 305 ASP cc_start: 0.7419 (t0) cc_final: 0.7114 (t0) REVERT: c 283 MET cc_start: 0.9010 (tpp) cc_final: 0.8500 (tpp) REVERT: c 305 ASP cc_start: 0.7405 (t0) cc_final: 0.6708 (p0) outliers start: 90 outliers final: 80 residues processed: 522 average time/residue: 0.4953 time to fit residues: 440.3030 Evaluate side-chains 506 residues out of total 4800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 426 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain M residue 312 VAL Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 304 ILE Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 221 LEU Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 221 LEU Chi-restraints excluded: chain P residue 304 ILE Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 304 ILE Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 304 ILE Chi-restraints excluded: chain S residue 312 VAL Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 312 VAL Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain U residue 418 MET Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 221 LEU Chi-restraints excluded: chain W residue 312 VAL Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 221 LEU Chi-restraints excluded: chain Y residue 304 ILE Chi-restraints excluded: chain Y residue 312 VAL Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 304 ILE Chi-restraints excluded: chain Z residue 312 VAL Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 221 LEU Chi-restraints excluded: chain a residue 312 VAL Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 221 LEU Chi-restraints excluded: chain c residue 304 ILE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain d residue 312 VAL Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 179 optimal weight: 2.9990 chunk 480 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 313 optimal weight: 0.6980 chunk 131 optimal weight: 0.8980 chunk 534 optimal weight: 2.9990 chunk 443 optimal weight: 0.5980 chunk 247 optimal weight: 0.4980 chunk 44 optimal weight: 0.4980 chunk 176 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 45144 Z= 0.205 Angle : 0.491 6.108 60888 Z= 0.260 Chirality : 0.042 0.139 7032 Planarity : 0.004 0.042 7944 Dihedral : 4.649 22.371 6240 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.19 % Allowed : 13.67 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.12), residues: 5616 helix: 2.75 (0.11), residues: 2280 sheet: -1.17 (0.15), residues: 984 loop : -0.53 (0.13), residues: 2352 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS W 399 PHE 0.013 0.002 PHE Q 437 TYR 0.005 0.001 TYR E 316 ARG 0.003 0.000 ARG S 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11232 Ramachandran restraints generated. 5616 Oldfield, 0 Emsley, 5616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 4800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 426 time to evaluate : 5.263 Fit side-chains REVERT: D 283 MET cc_start: 0.8996 (tpp) cc_final: 0.8526 (tpp) REVERT: E 283 MET cc_start: 0.8998 (tpp) cc_final: 0.8525 (tpp) REVERT: F 283 MET cc_start: 0.8970 (tpp) cc_final: 0.8507 (tpp) REVERT: J 283 MET cc_start: 0.9001 (tpp) cc_final: 0.8543 (tpp) REVERT: J 305 ASP cc_start: 0.7288 (t0) cc_final: 0.7025 (t0) REVERT: K 283 MET cc_start: 0.8998 (tpp) cc_final: 0.8529 (tpp) REVERT: L 283 MET cc_start: 0.8976 (tpp) cc_final: 0.8496 (tpp) REVERT: M 283 MET cc_start: 0.8997 (tpp) cc_final: 0.8532 (tpp) REVERT: M 305 ASP cc_start: 0.7290 (t0) cc_final: 0.7021 (t0) REVERT: N 283 MET cc_start: 0.8999 (tpp) cc_final: 0.8530 (tpp) REVERT: O 283 MET cc_start: 0.9018 (tpp) cc_final: 0.8512 (tpp) REVERT: P 283 MET cc_start: 0.8964 (tpp) cc_final: 0.8492 (tpp) REVERT: Q 238 GLN cc_start: 0.7826 (tp40) cc_final: 0.7474 (tm-30) REVERT: Q 283 MET cc_start: 0.8996 (tpp) cc_final: 0.8504 (tpp) REVERT: Q 305 ASP cc_start: 0.7240 (t0) cc_final: 0.6982 (t0) REVERT: R 283 MET cc_start: 0.9042 (tpp) cc_final: 0.8549 (tpp) REVERT: S 283 MET cc_start: 0.8970 (tpp) cc_final: 0.8513 (tpp) REVERT: T 283 MET cc_start: 0.8966 (tpp) cc_final: 0.8486 (tpp) REVERT: U 283 MET cc_start: 0.9008 (tpp) cc_final: 0.8535 (tpp) REVERT: V 283 MET cc_start: 0.8995 (tpp) cc_final: 0.8534 (tpp) REVERT: W 283 MET cc_start: 0.8986 (tpp) cc_final: 0.8521 (tpp) REVERT: X 283 MET cc_start: 0.8975 (tpp) cc_final: 0.8501 (tpp) REVERT: Y 283 MET cc_start: 0.8995 (tpp) cc_final: 0.8531 (tpp) REVERT: Y 305 ASP cc_start: 0.7288 (t0) cc_final: 0.7014 (t0) REVERT: Z 283 MET cc_start: 0.8996 (tpp) cc_final: 0.8528 (tpp) REVERT: Z 305 ASP cc_start: 0.7281 (t0) cc_final: 0.7008 (t0) REVERT: a 283 MET cc_start: 0.8992 (tpp) cc_final: 0.8521 (tpp) REVERT: b 283 MET cc_start: 0.8998 (tpp) cc_final: 0.8537 (tpp) REVERT: c 283 MET cc_start: 0.8969 (tpp) cc_final: 0.8491 (tpp) REVERT: d 283 MET cc_start: 0.8992 (tpp) cc_final: 0.8516 (tpp) outliers start: 153 outliers final: 85 residues processed: 554 average time/residue: 0.4495 time to fit residues: 426.9853 Evaluate side-chains 501 residues out of total 4800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 416 time to evaluate : 4.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 304 ILE Chi-restraints excluded: chain D residue 312 VAL Chi-restraints excluded: chain D residue 352 LEU Chi-restraints excluded: chain E residue 221 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 352 LEU Chi-restraints excluded: chain F residue 221 LEU Chi-restraints excluded: chain F residue 312 VAL Chi-restraints excluded: chain F residue 352 LEU Chi-restraints excluded: chain J residue 221 LEU Chi-restraints excluded: chain J residue 304 ILE Chi-restraints excluded: chain J residue 312 VAL Chi-restraints excluded: chain J residue 352 LEU Chi-restraints excluded: chain K residue 221 LEU Chi-restraints excluded: chain K residue 304 ILE Chi-restraints excluded: chain K residue 312 VAL Chi-restraints excluded: chain K residue 352 LEU Chi-restraints excluded: chain L residue 221 LEU Chi-restraints excluded: chain L residue 312 VAL Chi-restraints excluded: chain L residue 352 LEU Chi-restraints excluded: chain M residue 221 LEU Chi-restraints excluded: chain M residue 304 ILE Chi-restraints excluded: chain M residue 312 VAL Chi-restraints excluded: chain M residue 352 LEU Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 304 ILE Chi-restraints excluded: chain N residue 312 VAL Chi-restraints excluded: chain N residue 352 LEU Chi-restraints excluded: chain O residue 221 LEU Chi-restraints excluded: chain O residue 312 VAL Chi-restraints excluded: chain O residue 352 LEU Chi-restraints excluded: chain P residue 221 LEU Chi-restraints excluded: chain P residue 304 ILE Chi-restraints excluded: chain P residue 312 VAL Chi-restraints excluded: chain P residue 352 LEU Chi-restraints excluded: chain Q residue 221 LEU Chi-restraints excluded: chain Q residue 304 ILE Chi-restraints excluded: chain Q residue 312 VAL Chi-restraints excluded: chain Q residue 352 LEU Chi-restraints excluded: chain R residue 221 LEU Chi-restraints excluded: chain R residue 312 VAL Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain S residue 221 LEU Chi-restraints excluded: chain S residue 304 ILE Chi-restraints excluded: chain S residue 312 VAL Chi-restraints excluded: chain S residue 352 LEU Chi-restraints excluded: chain T residue 221 LEU Chi-restraints excluded: chain T residue 304 ILE Chi-restraints excluded: chain T residue 312 VAL Chi-restraints excluded: chain T residue 352 LEU Chi-restraints excluded: chain U residue 221 LEU Chi-restraints excluded: chain U residue 312 VAL Chi-restraints excluded: chain U residue 352 LEU Chi-restraints excluded: chain U residue 418 MET Chi-restraints excluded: chain V residue 221 LEU Chi-restraints excluded: chain V residue 312 VAL Chi-restraints excluded: chain V residue 352 LEU Chi-restraints excluded: chain W residue 221 LEU Chi-restraints excluded: chain W residue 312 VAL Chi-restraints excluded: chain W residue 352 LEU Chi-restraints excluded: chain X residue 221 LEU Chi-restraints excluded: chain X residue 312 VAL Chi-restraints excluded: chain X residue 352 LEU Chi-restraints excluded: chain Y residue 221 LEU Chi-restraints excluded: chain Y residue 304 ILE Chi-restraints excluded: chain Y residue 312 VAL Chi-restraints excluded: chain Y residue 352 LEU Chi-restraints excluded: chain Z residue 221 LEU Chi-restraints excluded: chain Z residue 304 ILE Chi-restraints excluded: chain Z residue 312 VAL Chi-restraints excluded: chain Z residue 352 LEU Chi-restraints excluded: chain a residue 221 LEU Chi-restraints excluded: chain a residue 312 VAL Chi-restraints excluded: chain a residue 352 LEU Chi-restraints excluded: chain b residue 221 LEU Chi-restraints excluded: chain b residue 312 VAL Chi-restraints excluded: chain b residue 352 LEU Chi-restraints excluded: chain c residue 221 LEU Chi-restraints excluded: chain c residue 304 ILE Chi-restraints excluded: chain c residue 312 VAL Chi-restraints excluded: chain c residue 352 LEU Chi-restraints excluded: chain d residue 221 LEU Chi-restraints excluded: chain d residue 312 VAL Chi-restraints excluded: chain d residue 352 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 552 random chunks: chunk 514 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 390 optimal weight: 1.9990 chunk 302 optimal weight: 1.9990 chunk 449 optimal weight: 0.7980 chunk 298 optimal weight: 0.9990 chunk 532 optimal weight: 1.9990 chunk 332 optimal weight: 0.9980 chunk 324 optimal weight: 0.7980 chunk 245 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: