Starting phenix.real_space_refine on Tue Jun 25 03:54:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/06_2024/8rmn_19365.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/06_2024/8rmn_19365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/06_2024/8rmn_19365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/06_2024/8rmn_19365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/06_2024/8rmn_19365.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rmn_19365/06_2024/8rmn_19365.pdb" } resolution = 3.8 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= 0.001 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 460 5.16 5 C 35480 2.51 5 N 9480 2.21 5 O 10020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 135": "OE1" <-> "OE2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A GLU 259": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 237": "OE1" <-> "OE2" Residue "B GLU 259": "OE1" <-> "OE2" Residue "C GLU 135": "OE1" <-> "OE2" Residue "C GLU 154": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 237": "OE1" <-> "OE2" Residue "C GLU 259": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 154": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 259": "OE1" <-> "OE2" Residue "E GLU 135": "OE1" <-> "OE2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E GLU 259": "OE1" <-> "OE2" Residue "F GLU 135": "OE1" <-> "OE2" Residue "F GLU 154": "OE1" <-> "OE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F GLU 237": "OE1" <-> "OE2" Residue "F GLU 259": "OE1" <-> "OE2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G GLU 155": "OE1" <-> "OE2" Residue "G GLU 237": "OE1" <-> "OE2" Residue "G GLU 259": "OE1" <-> "OE2" Residue "H GLU 135": "OE1" <-> "OE2" Residue "H GLU 154": "OE1" <-> "OE2" Residue "H GLU 155": "OE1" <-> "OE2" Residue "H GLU 237": "OE1" <-> "OE2" Residue "H GLU 259": "OE1" <-> "OE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I GLU 154": "OE1" <-> "OE2" Residue "I GLU 155": "OE1" <-> "OE2" Residue "I GLU 237": "OE1" <-> "OE2" Residue "I GLU 259": "OE1" <-> "OE2" Residue "J GLU 135": "OE1" <-> "OE2" Residue "J GLU 154": "OE1" <-> "OE2" Residue "J GLU 155": "OE1" <-> "OE2" Residue "J GLU 237": "OE1" <-> "OE2" Residue "J GLU 259": "OE1" <-> "OE2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "K GLU 154": "OE1" <-> "OE2" Residue "K GLU 155": "OE1" <-> "OE2" Residue "K GLU 237": "OE1" <-> "OE2" Residue "K GLU 259": "OE1" <-> "OE2" Residue "L GLU 135": "OE1" <-> "OE2" Residue "L GLU 154": "OE1" <-> "OE2" Residue "L GLU 155": "OE1" <-> "OE2" Residue "L GLU 237": "OE1" <-> "OE2" Residue "L GLU 259": "OE1" <-> "OE2" Residue "M GLU 135": "OE1" <-> "OE2" Residue "M GLU 154": "OE1" <-> "OE2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M GLU 237": "OE1" <-> "OE2" Residue "M GLU 259": "OE1" <-> "OE2" Residue "N GLU 135": "OE1" <-> "OE2" Residue "N GLU 154": "OE1" <-> "OE2" Residue "N GLU 155": "OE1" <-> "OE2" Residue "N GLU 237": "OE1" <-> "OE2" Residue "N GLU 259": "OE1" <-> "OE2" Residue "O GLU 135": "OE1" <-> "OE2" Residue "O GLU 154": "OE1" <-> "OE2" Residue "O GLU 155": "OE1" <-> "OE2" Residue "O GLU 237": "OE1" <-> "OE2" Residue "O GLU 259": "OE1" <-> "OE2" Residue "P GLU 135": "OE1" <-> "OE2" Residue "P GLU 154": "OE1" <-> "OE2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "P GLU 237": "OE1" <-> "OE2" Residue "P GLU 259": "OE1" <-> "OE2" Residue "Q GLU 135": "OE1" <-> "OE2" Residue "Q GLU 154": "OE1" <-> "OE2" Residue "Q GLU 155": "OE1" <-> "OE2" Residue "Q GLU 237": "OE1" <-> "OE2" Residue "Q GLU 259": "OE1" <-> "OE2" Residue "R GLU 135": "OE1" <-> "OE2" Residue "R GLU 154": "OE1" <-> "OE2" Residue "R GLU 155": "OE1" <-> "OE2" Residue "R GLU 237": "OE1" <-> "OE2" Residue "R GLU 259": "OE1" <-> "OE2" Residue "S GLU 135": "OE1" <-> "OE2" Residue "S GLU 154": "OE1" <-> "OE2" Residue "S GLU 155": "OE1" <-> "OE2" Residue "S GLU 237": "OE1" <-> "OE2" Residue "S GLU 259": "OE1" <-> "OE2" Residue "T GLU 135": "OE1" <-> "OE2" Residue "T GLU 154": "OE1" <-> "OE2" Residue "T GLU 155": "OE1" <-> "OE2" Residue "T GLU 237": "OE1" <-> "OE2" Residue "T GLU 259": "OE1" <-> "OE2" Residue "e ARG 35": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 55440 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "U" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "B" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "C" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "D" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "E" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "F" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "G" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "H" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "I" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "J" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "K" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "L" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "M" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "N" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "O" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "P" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "Q" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "R" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "S" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "T" Number of atoms: 2039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2039 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain breaks: 1 Chain: "V" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "W" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "X" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "Y" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "Z" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "a" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "b" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "c" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "d" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "e" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "f" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "g" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "h" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "i" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "j" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "k" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "l" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "m" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Chain: "n" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain breaks: 4 Time building chain proxies: 22.77, per 1000 atoms: 0.41 Number of scatterers: 55440 At special positions: 0 Unit cell: (138.012, 143.871, 254.541, 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 460 16.00 O 10020 8.00 N 9480 7.00 C 35480 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 162 " distance=2.02 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 162 " distance=2.02 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 162 " distance=2.02 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 162 " distance=2.02 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 162 " distance=2.02 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 162 " distance=2.02 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 162 " distance=2.02 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 162 " distance=2.02 Simple disulfide: pdb=" SG CYS I 41 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 43 " - pdb=" SG CYS I 162 " distance=2.02 Simple disulfide: pdb=" SG CYS J 41 " - pdb=" SG CYS J 131 " distance=2.03 Simple disulfide: pdb=" SG CYS J 43 " - pdb=" SG CYS J 162 " distance=2.02 Simple disulfide: pdb=" SG CYS K 41 " - pdb=" SG CYS K 131 " distance=2.03 Simple disulfide: pdb=" SG CYS K 43 " - pdb=" SG CYS K 162 " distance=2.02 Simple disulfide: pdb=" SG CYS L 41 " - pdb=" SG CYS L 131 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 162 " distance=2.02 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 131 " distance=2.03 Simple disulfide: pdb=" SG CYS M 43 " - pdb=" SG CYS M 162 " distance=2.02 Simple disulfide: pdb=" SG CYS N 41 " - pdb=" SG CYS N 131 " distance=2.03 Simple disulfide: pdb=" SG CYS N 43 " - pdb=" SG CYS N 162 " distance=2.02 Simple disulfide: pdb=" SG CYS O 41 " - pdb=" SG CYS O 131 " distance=2.03 Simple disulfide: pdb=" SG CYS O 43 " - pdb=" SG CYS O 162 " distance=2.02 Simple disulfide: pdb=" SG CYS P 41 " - pdb=" SG CYS P 131 " distance=2.03 Simple disulfide: pdb=" SG CYS P 43 " - pdb=" SG CYS P 162 " distance=2.02 Simple disulfide: pdb=" SG CYS Q 41 " - pdb=" SG CYS Q 131 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 43 " - pdb=" SG CYS Q 162 " distance=2.02 Simple disulfide: pdb=" SG CYS R 41 " - pdb=" SG CYS R 131 " distance=2.03 Simple disulfide: pdb=" SG CYS R 43 " - pdb=" SG CYS R 162 " distance=2.02 Simple disulfide: pdb=" SG CYS S 41 " - pdb=" SG CYS S 131 " distance=2.03 Simple disulfide: pdb=" SG CYS S 43 " - pdb=" SG CYS S 162 " distance=2.02 Simple disulfide: pdb=" SG CYS T 41 " - pdb=" SG CYS T 131 " distance=2.03 Simple disulfide: pdb=" SG CYS T 43 " - pdb=" SG CYS T 162 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 16.81 Conformation dependent library (CDL) restraints added in 8.0 seconds 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13320 Finding SS restraints... Secondary structure from input PDB file: 260 helices and 40 sheets defined 63.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 5 through 14 Processing helix chain 'A' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE A 19 " --> pdb=" O ASN A 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 39 " --> pdb=" O SER A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 70 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP A 75 " --> pdb=" O ARG A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Proline residue: A 115 - end of helix removed outlier: 4.322A pdb=" N TRP A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP A 146 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 170 through 211 Processing helix chain 'A' and resid 214 through 253 Processing helix chain 'A' and resid 268 through 276 Processing helix chain 'U' and resid 62 through 65 Processing helix chain 'U' and resid 87 through 91 Processing helix chain 'B' and resid 6 through 14 Processing helix chain 'B' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE B 19 " --> pdb=" O ASN B 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE B 39 " --> pdb=" O SER B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 70 Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) Proline residue: B 115 - end of helix removed outlier: 4.323A pdb=" N TRP B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.590A pdb=" N ASP B 146 " --> pdb=" O PRO B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 160 Processing helix chain 'B' and resid 170 through 211 Processing helix chain 'B' and resid 214 through 253 Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'C' and resid 6 through 14 Processing helix chain 'C' and resid 15 through 39 removed outlier: 4.004A pdb=" N ILE C 19 " --> pdb=" O ASN C 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 39 " --> pdb=" O SER C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 70 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP C 75 " --> pdb=" O ARG C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) Proline residue: C 115 - end of helix removed outlier: 4.323A pdb=" N TRP C 118 " --> pdb=" O ALA C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.590A pdb=" N ASP C 146 " --> pdb=" O PRO C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 160 Processing helix chain 'C' and resid 170 through 211 Processing helix chain 'C' and resid 214 through 253 Processing helix chain 'C' and resid 268 through 276 Processing helix chain 'D' and resid 6 through 14 Processing helix chain 'D' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE D 19 " --> pdb=" O ASN D 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 70 Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP D 75 " --> pdb=" O ARG D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) Proline residue: D 115 - end of helix removed outlier: 4.322A pdb=" N TRP D 118 " --> pdb=" O ALA D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.590A pdb=" N ASP D 146 " --> pdb=" O PRO D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 Processing helix chain 'D' and resid 170 through 211 Processing helix chain 'D' and resid 214 through 253 Processing helix chain 'D' and resid 268 through 276 Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE E 19 " --> pdb=" O ASN E 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE E 39 " --> pdb=" O SER E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 70 Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP E 75 " --> pdb=" O ARG E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) Proline residue: E 115 - end of helix removed outlier: 4.323A pdb=" N TRP E 118 " --> pdb=" O ALA E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 142 through 146 removed outlier: 3.592A pdb=" N ASP E 146 " --> pdb=" O PRO E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 151 through 160 Processing helix chain 'E' and resid 170 through 211 Processing helix chain 'E' and resid 214 through 253 Processing helix chain 'E' and resid 268 through 276 Processing helix chain 'F' and resid 6 through 14 Processing helix chain 'F' and resid 15 through 39 removed outlier: 4.004A pdb=" N ILE F 19 " --> pdb=" O ASN F 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE F 39 " --> pdb=" O SER F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 70 Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP F 75 " --> pdb=" O ARG F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) Proline residue: F 115 - end of helix removed outlier: 4.322A pdb=" N TRP F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP F 146 " --> pdb=" O PRO F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 160 Processing helix chain 'F' and resid 170 through 211 Processing helix chain 'F' and resid 214 through 253 Processing helix chain 'F' and resid 268 through 276 Processing helix chain 'G' and resid 6 through 14 Processing helix chain 'G' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE G 19 " --> pdb=" O ASN G 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE G 39 " --> pdb=" O SER G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 70 Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP G 75 " --> pdb=" O ARG G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) Proline residue: G 115 - end of helix removed outlier: 4.322A pdb=" N TRP G 118 " --> pdb=" O ALA G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 134 Processing helix chain 'G' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP G 146 " --> pdb=" O PRO G 143 " (cutoff:3.500A) Processing helix chain 'G' and resid 151 through 160 Processing helix chain 'G' and resid 170 through 211 Processing helix chain 'G' and resid 214 through 253 Processing helix chain 'G' and resid 268 through 276 Processing helix chain 'H' and resid 6 through 14 Processing helix chain 'H' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE H 19 " --> pdb=" O ASN H 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 70 Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP H 75 " --> pdb=" O ARG H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) Proline residue: H 115 - end of helix removed outlier: 4.322A pdb=" N TRP H 118 " --> pdb=" O ALA H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 134 Processing helix chain 'H' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP H 146 " --> pdb=" O PRO H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 160 Processing helix chain 'H' and resid 170 through 211 Processing helix chain 'H' and resid 214 through 253 Processing helix chain 'H' and resid 268 through 276 Processing helix chain 'I' and resid 6 through 14 Processing helix chain 'I' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE I 19 " --> pdb=" O ASN I 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE I 39 " --> pdb=" O SER I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 70 Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP I 75 " --> pdb=" O ARG I 71 " (cutoff:3.500A) Processing helix chain 'I' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) Proline residue: I 115 - end of helix removed outlier: 4.322A pdb=" N TRP I 118 " --> pdb=" O ALA I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 134 Processing helix chain 'I' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP I 146 " --> pdb=" O PRO I 143 " (cutoff:3.500A) Processing helix chain 'I' and resid 151 through 160 Processing helix chain 'I' and resid 170 through 211 Processing helix chain 'I' and resid 214 through 253 Processing helix chain 'I' and resid 268 through 276 Processing helix chain 'J' and resid 6 through 14 Processing helix chain 'J' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE J 19 " --> pdb=" O ASN J 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE J 39 " --> pdb=" O SER J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 48 through 70 Proline residue: J 59 - end of helix Processing helix chain 'J' and resid 71 through 82 removed outlier: 3.632A pdb=" N TRP J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG J 110 " --> pdb=" O SER J 106 " (cutoff:3.500A) Proline residue: J 115 - end of helix removed outlier: 4.322A pdb=" N TRP J 118 " --> pdb=" O ALA J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 134 Processing helix chain 'J' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP J 146 " --> pdb=" O PRO J 143 " (cutoff:3.500A) Processing helix chain 'J' and resid 151 through 160 Processing helix chain 'J' and resid 170 through 211 Processing helix chain 'J' and resid 214 through 253 Processing helix chain 'J' and resid 268 through 276 Processing helix chain 'K' and resid 6 through 14 Processing helix chain 'K' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE K 19 " --> pdb=" O ASN K 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE K 39 " --> pdb=" O SER K 35 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 70 Proline residue: K 59 - end of helix Processing helix chain 'K' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG K 110 " --> pdb=" O SER K 106 " (cutoff:3.500A) Proline residue: K 115 - end of helix removed outlier: 4.322A pdb=" N TRP K 118 " --> pdb=" O ALA K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 126 through 134 Processing helix chain 'K' and resid 142 through 146 removed outlier: 3.590A pdb=" N ASP K 146 " --> pdb=" O PRO K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 151 through 160 Processing helix chain 'K' and resid 170 through 211 Processing helix chain 'K' and resid 214 through 253 Processing helix chain 'K' and resid 268 through 276 Processing helix chain 'L' and resid 6 through 14 Processing helix chain 'L' and resid 15 through 39 removed outlier: 4.004A pdb=" N ILE L 19 " --> pdb=" O ASN L 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE L 39 " --> pdb=" O SER L 35 " (cutoff:3.500A) Processing helix chain 'L' and resid 48 through 70 Proline residue: L 59 - end of helix Processing helix chain 'L' and resid 71 through 82 removed outlier: 3.632A pdb=" N TRP L 75 " --> pdb=" O ARG L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 126 removed outlier: 4.349A pdb=" N ARG L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Proline residue: L 115 - end of helix removed outlier: 4.322A pdb=" N TRP L 118 " --> pdb=" O ALA L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 134 Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP L 146 " --> pdb=" O PRO L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 151 through 160 Processing helix chain 'L' and resid 170 through 211 Processing helix chain 'L' and resid 214 through 253 Processing helix chain 'L' and resid 268 through 276 Processing helix chain 'M' and resid 6 through 14 Processing helix chain 'M' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE M 19 " --> pdb=" O ASN M 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE M 39 " --> pdb=" O SER M 35 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 70 Proline residue: M 59 - end of helix Processing helix chain 'M' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP M 75 " --> pdb=" O ARG M 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG M 110 " --> pdb=" O SER M 106 " (cutoff:3.500A) Proline residue: M 115 - end of helix removed outlier: 4.322A pdb=" N TRP M 118 " --> pdb=" O ALA M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 126 through 134 Processing helix chain 'M' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP M 146 " --> pdb=" O PRO M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 151 through 160 Processing helix chain 'M' and resid 170 through 211 Processing helix chain 'M' and resid 214 through 253 Processing helix chain 'M' and resid 268 through 276 Processing helix chain 'N' and resid 6 through 14 Processing helix chain 'N' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE N 19 " --> pdb=" O ASN N 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE N 39 " --> pdb=" O SER N 35 " (cutoff:3.500A) Processing helix chain 'N' and resid 48 through 70 Proline residue: N 59 - end of helix Processing helix chain 'N' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG N 110 " --> pdb=" O SER N 106 " (cutoff:3.500A) Proline residue: N 115 - end of helix removed outlier: 4.322A pdb=" N TRP N 118 " --> pdb=" O ALA N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 134 Processing helix chain 'N' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP N 146 " --> pdb=" O PRO N 143 " (cutoff:3.500A) Processing helix chain 'N' and resid 151 through 160 Processing helix chain 'N' and resid 170 through 211 Processing helix chain 'N' and resid 214 through 253 Processing helix chain 'N' and resid 268 through 276 Processing helix chain 'O' and resid 6 through 14 Processing helix chain 'O' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE O 19 " --> pdb=" O ASN O 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE O 39 " --> pdb=" O SER O 35 " (cutoff:3.500A) Processing helix chain 'O' and resid 48 through 70 Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP O 75 " --> pdb=" O ARG O 71 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG O 110 " --> pdb=" O SER O 106 " (cutoff:3.500A) Proline residue: O 115 - end of helix removed outlier: 4.322A pdb=" N TRP O 118 " --> pdb=" O ALA O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 126 through 134 Processing helix chain 'O' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP O 146 " --> pdb=" O PRO O 143 " (cutoff:3.500A) Processing helix chain 'O' and resid 151 through 160 Processing helix chain 'O' and resid 170 through 211 Processing helix chain 'O' and resid 214 through 253 Processing helix chain 'O' and resid 268 through 276 Processing helix chain 'P' and resid 6 through 14 Processing helix chain 'P' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE P 19 " --> pdb=" O ASN P 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE P 39 " --> pdb=" O SER P 35 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 70 Proline residue: P 59 - end of helix Processing helix chain 'P' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP P 75 " --> pdb=" O ARG P 71 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG P 110 " --> pdb=" O SER P 106 " (cutoff:3.500A) Proline residue: P 115 - end of helix removed outlier: 4.323A pdb=" N TRP P 118 " --> pdb=" O ALA P 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 126 through 134 Processing helix chain 'P' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP P 146 " --> pdb=" O PRO P 143 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 160 Processing helix chain 'P' and resid 170 through 211 Processing helix chain 'P' and resid 214 through 253 Processing helix chain 'P' and resid 268 through 276 Processing helix chain 'Q' and resid 6 through 14 Processing helix chain 'Q' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE Q 39 " --> pdb=" O SER Q 35 " (cutoff:3.500A) Processing helix chain 'Q' and resid 48 through 70 Proline residue: Q 59 - end of helix Processing helix chain 'Q' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP Q 75 " --> pdb=" O ARG Q 71 " (cutoff:3.500A) Processing helix chain 'Q' and resid 95 through 126 removed outlier: 4.351A pdb=" N ARG Q 110 " --> pdb=" O SER Q 106 " (cutoff:3.500A) Proline residue: Q 115 - end of helix removed outlier: 4.323A pdb=" N TRP Q 118 " --> pdb=" O ALA Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 126 through 134 Processing helix chain 'Q' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP Q 146 " --> pdb=" O PRO Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 151 through 160 Processing helix chain 'Q' and resid 170 through 211 Processing helix chain 'Q' and resid 214 through 253 Processing helix chain 'Q' and resid 268 through 276 Processing helix chain 'R' and resid 6 through 14 Processing helix chain 'R' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE R 19 " --> pdb=" O ASN R 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE R 39 " --> pdb=" O SER R 35 " (cutoff:3.500A) Processing helix chain 'R' and resid 48 through 70 Proline residue: R 59 - end of helix Processing helix chain 'R' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP R 75 " --> pdb=" O ARG R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG R 110 " --> pdb=" O SER R 106 " (cutoff:3.500A) Proline residue: R 115 - end of helix removed outlier: 4.322A pdb=" N TRP R 118 " --> pdb=" O ALA R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 134 Processing helix chain 'R' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP R 146 " --> pdb=" O PRO R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 160 Processing helix chain 'R' and resid 170 through 211 Processing helix chain 'R' and resid 214 through 253 Processing helix chain 'R' and resid 268 through 276 Processing helix chain 'S' and resid 6 through 14 Processing helix chain 'S' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE S 19 " --> pdb=" O ASN S 15 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE S 39 " --> pdb=" O SER S 35 " (cutoff:3.500A) Processing helix chain 'S' and resid 48 through 70 Proline residue: S 59 - end of helix Processing helix chain 'S' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP S 75 " --> pdb=" O ARG S 71 " (cutoff:3.500A) Processing helix chain 'S' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG S 110 " --> pdb=" O SER S 106 " (cutoff:3.500A) Proline residue: S 115 - end of helix removed outlier: 4.321A pdb=" N TRP S 118 " --> pdb=" O ALA S 114 " (cutoff:3.500A) Processing helix chain 'S' and resid 126 through 134 Processing helix chain 'S' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP S 146 " --> pdb=" O PRO S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 151 through 160 Processing helix chain 'S' and resid 170 through 211 Processing helix chain 'S' and resid 214 through 253 Processing helix chain 'S' and resid 268 through 276 Processing helix chain 'T' and resid 6 through 14 Processing helix chain 'T' and resid 15 through 39 removed outlier: 4.003A pdb=" N ILE T 19 " --> pdb=" O ASN T 15 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE T 39 " --> pdb=" O SER T 35 " (cutoff:3.500A) Processing helix chain 'T' and resid 48 through 70 Proline residue: T 59 - end of helix Processing helix chain 'T' and resid 71 through 82 removed outlier: 3.631A pdb=" N TRP T 75 " --> pdb=" O ARG T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 95 through 126 removed outlier: 4.350A pdb=" N ARG T 110 " --> pdb=" O SER T 106 " (cutoff:3.500A) Proline residue: T 115 - end of helix removed outlier: 4.322A pdb=" N TRP T 118 " --> pdb=" O ALA T 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 126 through 134 Processing helix chain 'T' and resid 142 through 146 removed outlier: 3.591A pdb=" N ASP T 146 " --> pdb=" O PRO T 143 " (cutoff:3.500A) Processing helix chain 'T' and resid 151 through 160 Processing helix chain 'T' and resid 170 through 211 Processing helix chain 'T' and resid 214 through 253 Processing helix chain 'T' and resid 268 through 276 Processing helix chain 'V' and resid 62 through 65 Processing helix chain 'V' and resid 87 through 91 Processing helix chain 'W' and resid 62 through 65 Processing helix chain 'W' and resid 87 through 91 Processing helix chain 'X' and resid 62 through 65 Processing helix chain 'X' and resid 87 through 91 Processing helix chain 'Y' and resid 62 through 65 Processing helix chain 'Y' and resid 87 through 91 Processing helix chain 'Z' and resid 62 through 65 Processing helix chain 'Z' and resid 87 through 91 Processing helix chain 'a' and resid 62 through 65 Processing helix chain 'a' and resid 87 through 91 Processing helix chain 'b' and resid 62 through 65 Processing helix chain 'b' and resid 87 through 91 Processing helix chain 'c' and resid 62 through 65 Processing helix chain 'c' and resid 87 through 91 Processing helix chain 'd' and resid 62 through 65 Processing helix chain 'd' and resid 87 through 91 Processing helix chain 'e' and resid 62 through 65 Processing helix chain 'e' and resid 87 through 91 Processing helix chain 'f' and resid 62 through 65 Processing helix chain 'f' and resid 87 through 91 Processing helix chain 'g' and resid 62 through 65 Processing helix chain 'g' and resid 87 through 91 Processing helix chain 'h' and resid 62 through 65 Processing helix chain 'h' and resid 87 through 91 Processing helix chain 'i' and resid 62 through 65 Processing helix chain 'i' and resid 87 through 91 Processing helix chain 'j' and resid 62 through 65 Processing helix chain 'j' and resid 87 through 91 Processing helix chain 'k' and resid 62 through 65 Processing helix chain 'k' and resid 87 through 91 Processing helix chain 'l' and resid 62 through 65 Processing helix chain 'l' and resid 87 through 91 Processing helix chain 'm' and resid 62 through 65 Processing helix chain 'm' and resid 87 through 91 Processing helix chain 'n' and resid 62 through 65 Processing helix chain 'n' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'U' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL U 5 " --> pdb=" O ALA U 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR U 78 " --> pdb=" O ASP U 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'U' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY U 10 " --> pdb=" O GLN U 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER U 114 " --> pdb=" O VAL U 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET U 34 " --> pdb=" O ALA U 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA U 50 " --> pdb=" O MET U 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'V' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL V 5 " --> pdb=" O ALA V 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR V 78 " --> pdb=" O ASP V 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'V' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY V 10 " --> pdb=" O GLN V 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER V 114 " --> pdb=" O VAL V 12 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET V 34 " --> pdb=" O ALA V 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA V 50 " --> pdb=" O MET V 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP V 36 " --> pdb=" O VAL V 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'W' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL W 5 " --> pdb=" O ALA W 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR W 78 " --> pdb=" O ASP W 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'W' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY W 10 " --> pdb=" O GLN W 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER W 114 " --> pdb=" O VAL W 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET W 34 " --> pdb=" O ALA W 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA W 50 " --> pdb=" O MET W 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP W 36 " --> pdb=" O VAL W 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL X 5 " --> pdb=" O ALA X 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR X 78 " --> pdb=" O ASP X 73 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY X 10 " --> pdb=" O GLN X 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER X 114 " --> pdb=" O VAL X 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET X 34 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA X 50 " --> pdb=" O MET X 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP X 36 " --> pdb=" O VAL X 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Y' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL Y 5 " --> pdb=" O ALA Y 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR Y 78 " --> pdb=" O ASP Y 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Y' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY Y 10 " --> pdb=" O GLN Y 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER Y 114 " --> pdb=" O VAL Y 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET Y 34 " --> pdb=" O ALA Y 50 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N ALA Y 50 " --> pdb=" O MET Y 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP Y 36 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Z' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL Z 5 " --> pdb=" O ALA Z 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR Z 78 " --> pdb=" O ASP Z 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Z' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY Z 10 " --> pdb=" O GLN Z 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER Z 114 " --> pdb=" O VAL Z 12 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET Z 34 " --> pdb=" O ALA Z 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA Z 50 " --> pdb=" O MET Z 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP Z 36 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'a' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL a 5 " --> pdb=" O ALA a 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR a 78 " --> pdb=" O ASP a 73 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'a' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY a 10 " --> pdb=" O GLN a 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER a 114 " --> pdb=" O VAL a 12 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET a 34 " --> pdb=" O ALA a 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA a 50 " --> pdb=" O MET a 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP a 36 " --> pdb=" O VAL a 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'b' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL b 5 " --> pdb=" O ALA b 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR b 78 " --> pdb=" O ASP b 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'b' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY b 10 " --> pdb=" O GLN b 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER b 114 " --> pdb=" O VAL b 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET b 34 " --> pdb=" O ALA b 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA b 50 " --> pdb=" O MET b 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP b 36 " --> pdb=" O VAL b 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'c' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL c 5 " --> pdb=" O ALA c 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR c 78 " --> pdb=" O ASP c 73 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'c' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY c 10 " --> pdb=" O GLN c 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER c 114 " --> pdb=" O VAL c 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET c 34 " --> pdb=" O ALA c 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA c 50 " --> pdb=" O MET c 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP c 36 " --> pdb=" O VAL c 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'd' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL d 5 " --> pdb=" O ALA d 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR d 78 " --> pdb=" O ASP d 73 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'd' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY d 10 " --> pdb=" O GLN d 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER d 114 " --> pdb=" O VAL d 12 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N MET d 34 " --> pdb=" O ALA d 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA d 50 " --> pdb=" O MET d 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP d 36 " --> pdb=" O VAL d 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'e' and resid 4 through 7 removed outlier: 3.723A pdb=" N VAL e 5 " --> pdb=" O ALA e 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR e 78 " --> pdb=" O ASP e 73 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'e' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY e 10 " --> pdb=" O GLN e 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER e 114 " --> pdb=" O VAL e 12 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N MET e 34 " --> pdb=" O ALA e 50 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA e 50 " --> pdb=" O MET e 34 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP e 36 " --> pdb=" O VAL e 48 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'f' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL f 5 " --> pdb=" O ALA f 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR f 78 " --> pdb=" O ASP f 73 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'f' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY f 10 " --> pdb=" O GLN f 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER f 114 " --> pdb=" O VAL f 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET f 34 " --> pdb=" O ALA f 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA f 50 " --> pdb=" O MET f 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP f 36 " --> pdb=" O VAL f 48 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL g 5 " --> pdb=" O ALA g 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR g 78 " --> pdb=" O ASP g 73 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'g' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY g 10 " --> pdb=" O GLN g 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER g 114 " --> pdb=" O VAL g 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET g 34 " --> pdb=" O ALA g 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA g 50 " --> pdb=" O MET g 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP g 36 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'h' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL h 5 " --> pdb=" O ALA h 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR h 78 " --> pdb=" O ASP h 73 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'h' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY h 10 " --> pdb=" O GLN h 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER h 114 " --> pdb=" O VAL h 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET h 34 " --> pdb=" O ALA h 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP h 36 " --> pdb=" O VAL h 48 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'i' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL i 5 " --> pdb=" O ALA i 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR i 78 " --> pdb=" O ASP i 73 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'i' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY i 10 " --> pdb=" O GLN i 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER i 114 " --> pdb=" O VAL i 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET i 34 " --> pdb=" O ALA i 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA i 50 " --> pdb=" O MET i 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP i 36 " --> pdb=" O VAL i 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'j' and resid 4 through 7 removed outlier: 3.725A pdb=" N VAL j 5 " --> pdb=" O ALA j 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR j 78 " --> pdb=" O ASP j 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'j' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY j 10 " --> pdb=" O GLN j 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER j 114 " --> pdb=" O VAL j 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET j 34 " --> pdb=" O ALA j 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA j 50 " --> pdb=" O MET j 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP j 36 " --> pdb=" O VAL j 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'k' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL k 5 " --> pdb=" O ALA k 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR k 78 " --> pdb=" O ASP k 73 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'k' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY k 10 " --> pdb=" O GLN k 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER k 114 " --> pdb=" O VAL k 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET k 34 " --> pdb=" O ALA k 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA k 50 " --> pdb=" O MET k 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP k 36 " --> pdb=" O VAL k 48 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'l' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL l 5 " --> pdb=" O ALA l 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR l 78 " --> pdb=" O ASP l 73 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'l' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY l 10 " --> pdb=" O GLN l 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER l 114 " --> pdb=" O VAL l 12 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N MET l 34 " --> pdb=" O ALA l 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA l 50 " --> pdb=" O MET l 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP l 36 " --> pdb=" O VAL l 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'm' and resid 4 through 7 removed outlier: 3.723A pdb=" N VAL m 5 " --> pdb=" O ALA m 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR m 78 " --> pdb=" O ASP m 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'm' and resid 10 through 13 removed outlier: 3.809A pdb=" N GLY m 10 " --> pdb=" O GLN m 110 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER m 114 " --> pdb=" O VAL m 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET m 34 " --> pdb=" O ALA m 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA m 50 " --> pdb=" O MET m 34 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N TRP m 36 " --> pdb=" O VAL m 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'n' and resid 4 through 7 removed outlier: 3.724A pdb=" N VAL n 5 " --> pdb=" O ALA n 23 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR n 78 " --> pdb=" O ASP n 73 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'n' and resid 10 through 13 removed outlier: 3.808A pdb=" N GLY n 10 " --> pdb=" O GLN n 110 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER n 114 " --> pdb=" O VAL n 12 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N MET n 34 " --> pdb=" O ALA n 50 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ALA n 50 " --> pdb=" O MET n 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TRP n 36 " --> pdb=" O VAL n 48 " (cutoff:3.500A) 3901 hydrogen bonds defined for protein. 11223 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: 21.80 Time building geometry restraints manager: 18.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17616 1.34 - 1.46: 12250 1.46 - 1.58: 26134 1.58 - 1.69: 0 1.69 - 1.81: 600 Bond restraints: 56600 Sorted by residual: bond pdb=" N ARG e 35 " pdb=" CA ARG e 35 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.23e-02 6.61e+03 7.16e+00 bond pdb=" N MET e 34 " pdb=" CA MET e 34 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.25e-02 6.40e+03 6.71e+00 bond pdb=" N TRP e 36 " pdb=" CA TRP e 36 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.23e-02 6.61e+03 6.36e+00 bond pdb=" N TYR A 51 " pdb=" CA TYR A 51 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.17e-02 7.31e+03 5.43e+00 bond pdb=" N TYR D 51 " pdb=" CA TYR D 51 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.17e-02 7.31e+03 5.07e+00 ... (remaining 56595 not shown) Histogram of bond angle deviations from ideal: 100.47 - 107.25: 1655 107.25 - 114.03: 31978 114.03 - 120.80: 25915 120.80 - 127.58: 16431 127.58 - 134.35: 641 Bond angle restraints: 76620 Sorted by residual: angle pdb=" CA GLN T 270 " pdb=" CB GLN T 270 " pdb=" CG GLN T 270 " ideal model delta sigma weight residual 114.10 119.88 -5.78 2.00e+00 2.50e-01 8.34e+00 angle pdb=" CA GLN I 270 " pdb=" CB GLN I 270 " pdb=" CG GLN I 270 " ideal model delta sigma weight residual 114.10 119.88 -5.78 2.00e+00 2.50e-01 8.34e+00 angle pdb=" CA GLN S 270 " pdb=" CB GLN S 270 " pdb=" CG GLN S 270 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.31e+00 angle pdb=" CA GLN B 270 " pdb=" CB GLN B 270 " pdb=" CG GLN B 270 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.31e+00 angle pdb=" CA GLN G 270 " pdb=" CB GLN G 270 " pdb=" CG GLN G 270 " ideal model delta sigma weight residual 114.10 119.86 -5.76 2.00e+00 2.50e-01 8.29e+00 ... (remaining 76615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 30565 17.96 - 35.91: 2275 35.91 - 53.87: 500 53.87 - 71.83: 99 71.83 - 89.79: 41 Dihedral angle restraints: 33480 sinusoidal: 12900 harmonic: 20580 Sorted by residual: dihedral pdb=" CD ARG e 35 " pdb=" NE ARG e 35 " pdb=" CZ ARG e 35 " pdb=" NH1 ARG e 35 " ideal model delta sinusoidal sigma weight residual 0.00 79.35 -79.35 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB GLU I 259 " pdb=" CG GLU I 259 " pdb=" CD GLU I 259 " pdb=" OE1 GLU I 259 " ideal model delta sinusoidal sigma weight residual 0.00 89.23 -89.23 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU M 259 " pdb=" CG GLU M 259 " pdb=" CD GLU M 259 " pdb=" OE1 GLU M 259 " ideal model delta sinusoidal sigma weight residual 0.00 89.20 -89.20 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 33477 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 7680 0.058 - 0.117: 991 0.117 - 0.175: 49 0.175 - 0.234: 0 0.234 - 0.292: 20 Chirality restraints: 8740 Sorted by residual: chirality pdb=" CG LEU Y 81 " pdb=" CB LEU Y 81 " pdb=" CD1 LEU Y 81 " pdb=" CD2 LEU Y 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CG LEU d 81 " pdb=" CB LEU d 81 " pdb=" CD1 LEU d 81 " pdb=" CD2 LEU d 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CG LEU Z 81 " pdb=" CB LEU Z 81 " pdb=" CD1 LEU Z 81 " pdb=" CD2 LEU Z 81 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 8737 not shown) Planarity restraints: 9540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG e 35 " 1.083 9.50e-02 1.11e+02 4.85e-01 1.42e+02 pdb=" NE ARG e 35 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG e 35 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG e 35 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG e 35 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG H 14 " -0.238 9.50e-02 1.11e+02 1.07e-01 7.15e+00 pdb=" NE ARG H 14 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG H 14 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 14 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG H 14 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 14 " 0.238 9.50e-02 1.11e+02 1.07e-01 7.15e+00 pdb=" NE ARG F 14 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG F 14 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG F 14 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG F 14 " 0.006 2.00e-02 2.50e+03 ... (remaining 9537 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 1018 2.69 - 3.24: 56565 3.24 - 3.79: 86419 3.79 - 4.35: 104153 4.35 - 4.90: 177265 Nonbonded interactions: 425420 Sorted by model distance: nonbonded pdb=" OH TYR I 142 " pdb=" OE1 GLU I 176 " model vdw 2.133 2.440 nonbonded pdb=" OH TYR N 142 " pdb=" OE1 GLU N 176 " model vdw 2.133 2.440 nonbonded pdb=" OH TYR D 142 " pdb=" OE1 GLU D 176 " model vdw 2.133 2.440 nonbonded pdb=" OH TYR E 142 " pdb=" OE1 GLU E 176 " model vdw 2.133 2.440 nonbonded pdb=" OH TYR K 142 " pdb=" OE1 GLU K 176 " model vdw 2.133 2.440 ... (remaining 425415 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' 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' } ncs_group { reference = 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' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 24.180 Check model and map are aligned: 0.310 Set scattering table: 0.380 Process input model: 112.610 Find NCS groups from input model: 4.120 Set up NCS constraints: 0.830 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 150.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.004 0.042 56600 Z= 0.268 Angle : 0.710 8.247 76620 Z= 0.373 Chirality : 0.041 0.292 8740 Planarity : 0.008 0.485 9540 Dihedral : 13.550 89.787 20040 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.16 % Allowed : 20.43 % Favored : 78.41 % 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: 2.54 (0.10), residues: 6820 helix: 2.56 (0.08), residues: 3920 sheet: 2.02 (0.15), residues: 880 loop : -0.26 (0.14), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 221 HIS 0.005 0.001 HIS Q 263 PHE 0.031 0.002 PHE T 160 TYR 0.013 0.002 TYR M 51 ARG 0.008 0.001 ARG O 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1013 time to evaluate : 4.525 Fit side-chains REVERT: B 105 PHE cc_start: 0.8086 (t80) cc_final: 0.7748 (t80) REVERT: B 238 GLN cc_start: 0.7850 (tt0) cc_final: 0.7598 (tt0) REVERT: C 96 GLU cc_start: 0.6054 (mp0) cc_final: 0.5072 (mt-10) REVERT: C 244 MET cc_start: 0.7719 (tpt) cc_final: 0.6995 (tpp) REVERT: D 244 MET cc_start: 0.8183 (tpt) cc_final: 0.7938 (tpt) REVERT: E 187 MET cc_start: 0.7573 (mmm) cc_final: 0.6416 (ttp) REVERT: F 47 LYS cc_start: 0.6651 (ptpt) cc_final: 0.6376 (pttt) REVERT: F 238 GLN cc_start: 0.7619 (tt0) cc_final: 0.6945 (tt0) REVERT: G 244 MET cc_start: 0.7886 (tpt) cc_final: 0.7616 (tpp) REVERT: H 244 MET cc_start: 0.8187 (tpt) cc_final: 0.7943 (tpp) REVERT: I 244 MET cc_start: 0.7925 (tpt) cc_final: 0.7500 (tpp) REVERT: J 244 MET cc_start: 0.7996 (tpt) cc_final: 0.7498 (tpp) REVERT: L 105 PHE cc_start: 0.8136 (t80) cc_final: 0.7913 (t80) REVERT: M 274 ASP cc_start: 0.7394 (m-30) cc_final: 0.7048 (m-30) REVERT: R 273 LYS cc_start: 0.8073 (tptp) cc_final: 0.7843 (mttp) REVERT: S 187 MET cc_start: 0.7165 (mmm) cc_final: 0.6049 (ttp) REVERT: S 244 MET cc_start: 0.7624 (tpt) cc_final: 0.7113 (tpt) REVERT: T 244 MET cc_start: 0.7550 (tpt) cc_final: 0.7292 (tpt) REVERT: W 107 GLN cc_start: 0.4224 (mm-40) cc_final: 0.3771 (mm110) REVERT: l 58 THR cc_start: 0.4915 (t) cc_final: 0.4685 (p) REVERT: m 58 THR cc_start: 0.4850 (t) cc_final: 0.4649 (p) outliers start: 70 outliers final: 38 residues processed: 1082 average time/residue: 0.5129 time to fit residues: 952.1979 Evaluate side-chains 822 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 784 time to evaluate : 4.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 271 ASP Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 271 ASP Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain H residue 154 GLU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 271 ASP Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain J residue 154 GLU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain L residue 154 GLU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 271 ASP Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 271 ASP Chi-restraints excluded: chain O residue 154 GLU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 271 ASP Chi-restraints excluded: chain P residue 154 GLU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain Q residue 154 GLU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain S residue 154 GLU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 271 ASP Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain h residue 70 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 591 optimal weight: 0.0970 chunk 530 optimal weight: 10.0000 chunk 294 optimal weight: 8.9990 chunk 181 optimal weight: 0.8980 chunk 357 optimal weight: 0.8980 chunk 283 optimal weight: 8.9990 chunk 548 optimal weight: 0.0870 chunk 212 optimal weight: 2.9990 chunk 333 optimal weight: 8.9990 chunk 408 optimal weight: 2.9990 chunk 635 optimal weight: 5.9990 overall best weight: 0.9958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 GLN B 6 ASN ** C 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN ** D 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 270 GLN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 ASN ** L 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 238 GLN ** M 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 270 GLN N 6 ASN ** O 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 238 GLN ** P 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 270 GLN Q 6 ASN Q 270 GLN ** R 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 270 GLN ** T 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 110 GLN W 110 GLN X 110 GLN Y 110 GLN Z 110 GLN a 110 GLN b 110 GLN c 110 GLN d 110 GLN e 110 GLN f 110 GLN g 110 GLN h 110 GLN i 110 GLN j 110 GLN k 110 GLN l 110 GLN m 110 GLN n 110 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 56600 Z= 0.174 Angle : 0.587 6.824 76620 Z= 0.304 Chirality : 0.037 0.213 8740 Planarity : 0.004 0.061 9540 Dihedral : 4.732 55.009 7704 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.44 % Allowed : 18.85 % Favored : 77.71 % 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: 2.62 (0.10), residues: 6820 helix: 2.64 (0.08), residues: 3940 sheet: 1.75 (0.14), residues: 980 loop : -0.27 (0.15), residues: 1900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 221 HIS 0.004 0.001 HIS e 33 PHE 0.025 0.002 PHE F 105 TYR 0.013 0.001 TYR N 129 ARG 0.007 0.001 ARG H 241 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1094 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 887 time to evaluate : 4.446 Fit side-chains revert: symmetry clash REVERT: B 230 GLU cc_start: 0.7924 (tt0) cc_final: 0.7656 (tm-30) REVERT: B 231 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8411 (mm) REVERT: B 244 MET cc_start: 0.8282 (tpt) cc_final: 0.7658 (tpp) REVERT: C 96 GLU cc_start: 0.5963 (mp0) cc_final: 0.5104 (mt-10) REVERT: C 244 MET cc_start: 0.7501 (tpt) cc_final: 0.7209 (tpp) REVERT: C 273 LYS cc_start: 0.8480 (ptmt) cc_final: 0.8240 (mttt) REVERT: D 238 GLN cc_start: 0.7989 (tt0) cc_final: 0.7698 (tt0) REVERT: D 244 MET cc_start: 0.8208 (tpt) cc_final: 0.7958 (tpt) REVERT: E 187 MET cc_start: 0.7504 (mmm) cc_final: 0.6378 (ttp) REVERT: G 244 MET cc_start: 0.7851 (tpt) cc_final: 0.7393 (tpp) REVERT: H 244 MET cc_start: 0.8096 (tpt) cc_final: 0.7829 (tpp) REVERT: I 244 MET cc_start: 0.7867 (tpt) cc_final: 0.7403 (tpp) REVERT: J 238 GLN cc_start: 0.7982 (tt0) cc_final: 0.7697 (tt0) REVERT: J 244 MET cc_start: 0.7905 (tpt) cc_final: 0.7459 (tpp) REVERT: K 6 ASN cc_start: 0.4473 (OUTLIER) cc_final: 0.4126 (p0) REVERT: K 238 GLN cc_start: 0.8086 (tt0) cc_final: 0.7883 (tt0) REVERT: L 229 ARG cc_start: 0.8654 (tpp80) cc_final: 0.7440 (mtm110) REVERT: M 270 GLN cc_start: 0.6176 (tp40) cc_final: 0.5896 (tp-100) REVERT: N 6 ASN cc_start: 0.4355 (OUTLIER) cc_final: 0.3815 (p0) REVERT: O 230 GLU cc_start: 0.7963 (tt0) cc_final: 0.7619 (tm-30) REVERT: Q 238 GLN cc_start: 0.7748 (tt0) cc_final: 0.7390 (tt0) REVERT: R 96 GLU cc_start: 0.5978 (mp0) cc_final: 0.5416 (mt-10) REVERT: R 244 MET cc_start: 0.7166 (tpp) cc_final: 0.6755 (tpp) REVERT: S 187 MET cc_start: 0.7224 (mmm) cc_final: 0.6096 (ttp) REVERT: S 244 MET cc_start: 0.7396 (tpt) cc_final: 0.6867 (tpp) REVERT: S 248 ILE cc_start: 0.8160 (pt) cc_final: 0.7918 (pt) REVERT: T 6 ASN cc_start: 0.4605 (t0) cc_final: 0.4262 (p0) REVERT: T 244 MET cc_start: 0.7428 (tpt) cc_final: 0.7060 (tpp) REVERT: h 35 ARG cc_start: 0.5209 (mtt90) cc_final: 0.4957 (mtt-85) REVERT: i 107 GLN cc_start: 0.5964 (tm-30) cc_final: 0.5345 (pm20) REVERT: m 58 THR cc_start: 0.5637 (t) cc_final: 0.5398 (p) REVERT: n 68 PHE cc_start: 0.5575 (m-80) cc_final: 0.5314 (m-80) outliers start: 207 outliers final: 118 residues processed: 1010 average time/residue: 0.4857 time to fit residues: 845.6853 Evaluate side-chains 872 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 751 time to evaluate : 5.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain U residue 70 ILE Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 6 ASN Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 224 HIS Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 224 HIS Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 99 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 6 ASN Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 99 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 250 LYS Chi-restraints excluded: chain N residue 6 ASN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain Q residue 47 LYS Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 70 ILE Chi-restraints excluded: chain X residue 70 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 70 ILE Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 70 ILE Chi-restraints excluded: chain a residue 70 ILE Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain b residue 70 ILE Chi-restraints excluded: chain c residue 70 ILE Chi-restraints excluded: chain c residue 90 ASP Chi-restraints excluded: chain d residue 70 ILE Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain f residue 70 ILE Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 70 ILE Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain h residue 70 ILE Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 70 ILE Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 70 ILE Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 70 ILE Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 70 ILE Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 70 ILE Chi-restraints excluded: chain n residue 90 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 353 optimal weight: 0.9990 chunk 197 optimal weight: 0.0370 chunk 529 optimal weight: 30.0000 chunk 432 optimal weight: 6.9990 chunk 175 optimal weight: 0.7980 chunk 636 optimal weight: 2.9990 chunk 687 optimal weight: 9.9990 chunk 567 optimal weight: 9.9990 chunk 631 optimal weight: 30.0000 chunk 217 optimal weight: 20.0000 chunk 510 optimal weight: 0.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN B 181 HIS C 6 ASN D 6 ASN E 6 ASN F 6 ASN F 238 GLN G 6 ASN G 238 GLN H 6 ASN H 238 GLN I 6 ASN J 6 ASN L 6 ASN M 6 ASN ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 6 ASN P 6 ASN ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 ASN S 181 HIS S 238 GLN T 6 ASN Z 59 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 56600 Z= 0.165 Angle : 0.553 7.009 76620 Z= 0.287 Chirality : 0.036 0.177 8740 Planarity : 0.003 0.039 9540 Dihedral : 3.893 29.446 7624 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.54 % Allowed : 19.10 % Favored : 77.36 % 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: 2.50 (0.10), residues: 6820 helix: 2.56 (0.08), residues: 4000 sheet: 1.54 (0.14), residues: 980 loop : -0.35 (0.15), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 47 HIS 0.003 0.001 HIS F 263 PHE 0.026 0.002 PHE F 105 TYR 0.011 0.001 TYR c 95 ARG 0.007 0.000 ARG Q 241 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1045 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 832 time to evaluate : 4.549 Fit side-chains revert: symmetry clash REVERT: U 52 TYR cc_start: 0.3538 (OUTLIER) cc_final: 0.2646 (m-10) REVERT: B 244 MET cc_start: 0.8248 (tpt) cc_final: 0.7771 (tpp) REVERT: C 96 GLU cc_start: 0.5950 (mp0) cc_final: 0.5157 (mt-10) REVERT: C 244 MET cc_start: 0.7509 (tpt) cc_final: 0.7074 (tpp) REVERT: D 238 GLN cc_start: 0.7942 (tt0) cc_final: 0.7637 (tt0) REVERT: D 244 MET cc_start: 0.8278 (tpt) cc_final: 0.7694 (tpp) REVERT: E 187 MET cc_start: 0.7493 (mmm) cc_final: 0.6342 (ttp) REVERT: F 238 GLN cc_start: 0.7701 (tt0) cc_final: 0.7367 (tt0) REVERT: G 244 MET cc_start: 0.7833 (tpt) cc_final: 0.7235 (tpp) REVERT: H 244 MET cc_start: 0.8134 (tpt) cc_final: 0.7839 (tpp) REVERT: I 244 MET cc_start: 0.7944 (tpt) cc_final: 0.7455 (tpp) REVERT: J 238 GLN cc_start: 0.7954 (tt0) cc_final: 0.7738 (tt0) REVERT: J 244 MET cc_start: 0.7802 (tpt) cc_final: 0.7291 (tpp) REVERT: K 238 GLN cc_start: 0.8034 (tt0) cc_final: 0.7754 (tt0) REVERT: M 238 GLN cc_start: 0.7416 (tt0) cc_final: 0.7145 (tt0) REVERT: O 230 GLU cc_start: 0.8022 (tt0) cc_final: 0.7671 (tm-30) REVERT: P 238 GLN cc_start: 0.8012 (tt0) cc_final: 0.7797 (tt0) REVERT: Q 238 GLN cc_start: 0.7733 (tt0) cc_final: 0.7417 (tt0) REVERT: R 244 MET cc_start: 0.7214 (tpp) cc_final: 0.6494 (tpp) REVERT: S 187 MET cc_start: 0.7301 (mmm) cc_final: 0.6256 (ttp) REVERT: S 244 MET cc_start: 0.7349 (tpt) cc_final: 0.6624 (tpp) REVERT: S 248 ILE cc_start: 0.8200 (pt) cc_final: 0.7978 (pt) REVERT: T 105 PHE cc_start: 0.8171 (t80) cc_final: 0.7829 (t80) REVERT: T 244 MET cc_start: 0.7439 (tpt) cc_final: 0.7008 (tpp) REVERT: V 34 MET cc_start: 0.2980 (mmm) cc_final: 0.2460 (mmm) REVERT: f 18 LEU cc_start: 0.4971 (OUTLIER) cc_final: 0.4353 (mp) REVERT: h 35 ARG cc_start: 0.5413 (mtt90) cc_final: 0.5110 (mtt-85) REVERT: k 34 MET cc_start: 0.2356 (mmm) cc_final: 0.1888 (mmm) REVERT: k 107 GLN cc_start: 0.5679 (tm-30) cc_final: 0.4892 (pm20) REVERT: m 58 THR cc_start: 0.5827 (t) cc_final: 0.5581 (p) outliers start: 213 outliers final: 137 residues processed: 948 average time/residue: 0.4758 time to fit residues: 779.3381 Evaluate side-chains 872 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 733 time to evaluate : 4.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 188 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 264 ILE Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 250 LYS Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 141 HIS Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 195 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 216 LEU Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 214 THR Chi-restraints excluded: chain Q residue 264 ILE Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 70 ILE Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain e residue 90 ASP Chi-restraints excluded: chain f residue 18 LEU Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain i residue 12 VAL Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 70 ILE Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 12 VAL Chi-restraints excluded: chain k residue 70 ILE Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 90 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 629 optimal weight: 40.0000 chunk 478 optimal weight: 3.9990 chunk 330 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 chunk 303 optimal weight: 5.9990 chunk 427 optimal weight: 4.9990 chunk 639 optimal weight: 30.0000 chunk 676 optimal weight: 9.9990 chunk 333 optimal weight: 9.9990 chunk 605 optimal weight: 20.0000 chunk 182 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 181 HIS D 181 HIS F 181 HIS H 181 HIS H 238 GLN I 181 HIS J 6 ASN K 181 HIS M 227 ASN O 181 HIS O 238 GLN P 6 ASN P 181 HIS ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 181 HIS Z 59 HIS ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 56600 Z= 0.417 Angle : 0.735 10.084 76620 Z= 0.388 Chirality : 0.044 0.242 8740 Planarity : 0.005 0.040 9540 Dihedral : 4.547 20.907 7620 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 6.21 % Allowed : 18.94 % Favored : 74.85 % 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: 1.69 (0.10), residues: 6820 helix: 1.93 (0.08), residues: 3900 sheet: 1.24 (0.15), residues: 980 loop : -0.60 (0.15), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP e 36 HIS 0.006 0.002 HIS h 33 PHE 0.033 0.003 PHE C 160 TYR 0.018 0.003 TYR F 220 ARG 0.008 0.001 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 374 poor density : 711 time to evaluate : 4.578 Fit side-chains REVERT: U 52 TYR cc_start: 0.4123 (OUTLIER) cc_final: 0.3421 (m-80) REVERT: B 22 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8676 (tm) REVERT: B 244 MET cc_start: 0.8348 (tpt) cc_final: 0.7784 (tpp) REVERT: C 104 PHE cc_start: 0.7001 (t80) cc_final: 0.6800 (t80) REVERT: C 244 MET cc_start: 0.7894 (tpt) cc_final: 0.7299 (tpp) REVERT: C 273 LYS cc_start: 0.8538 (ptmt) cc_final: 0.8312 (mttt) REVERT: D 238 GLN cc_start: 0.8150 (tt0) cc_final: 0.7885 (tt0) REVERT: D 244 MET cc_start: 0.8289 (tpt) cc_final: 0.7732 (tpp) REVERT: E 22 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8705 (tm) REVERT: E 244 MET cc_start: 0.7838 (tpp) cc_final: 0.7485 (tpp) REVERT: G 22 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8690 (tm) REVERT: G 244 MET cc_start: 0.7976 (tpt) cc_final: 0.7318 (tpp) REVERT: H 244 MET cc_start: 0.8187 (tpt) cc_final: 0.7842 (tpp) REVERT: I 104 PHE cc_start: 0.6933 (t80) cc_final: 0.6726 (t80) REVERT: I 244 MET cc_start: 0.8173 (tpt) cc_final: 0.7688 (tpp) REVERT: J 22 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8777 (tm) REVERT: J 104 PHE cc_start: 0.6898 (t80) cc_final: 0.6694 (t80) REVERT: J 105 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7942 (t80) REVERT: J 238 GLN cc_start: 0.8169 (tt0) cc_final: 0.7958 (tt0) REVERT: J 244 MET cc_start: 0.7980 (tpt) cc_final: 0.7623 (tpp) REVERT: K 238 GLN cc_start: 0.8210 (tt0) cc_final: 0.7953 (tt0) REVERT: L 22 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8644 (tm) REVERT: L 104 PHE cc_start: 0.7011 (t80) cc_final: 0.6730 (t80) REVERT: L 244 MET cc_start: 0.8156 (tpt) cc_final: 0.7583 (tpp) REVERT: M 104 PHE cc_start: 0.6825 (t80) cc_final: 0.6587 (t80) REVERT: O 22 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8775 (tm) REVERT: P 238 GLN cc_start: 0.8215 (tt0) cc_final: 0.8005 (tt0) REVERT: Q 22 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8686 (tm) REVERT: Q 238 GLN cc_start: 0.8030 (tt0) cc_final: 0.7811 (tt0) REVERT: R 6 ASN cc_start: 0.4480 (t160) cc_final: 0.4069 (p0) REVERT: S 104 PHE cc_start: 0.6970 (t80) cc_final: 0.6750 (t80) REVERT: S 105 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.8027 (t80) REVERT: S 244 MET cc_start: 0.7793 (tpt) cc_final: 0.7283 (tpp) REVERT: T 22 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8773 (tm) REVERT: T 244 MET cc_start: 0.7829 (tpt) cc_final: 0.7253 (tpp) REVERT: W 107 GLN cc_start: 0.5759 (tm-30) cc_final: 0.4625 (pm20) REVERT: i 107 GLN cc_start: 0.5585 (tm-30) cc_final: 0.4642 (pm20) REVERT: k 34 MET cc_start: 0.3414 (OUTLIER) cc_final: 0.3033 (mmm) REVERT: l 19 ARG cc_start: 0.6245 (tpt170) cc_final: 0.5617 (tpp80) REVERT: m 58 THR cc_start: 0.5698 (t) cc_final: 0.5482 (p) outliers start: 374 outliers final: 255 residues processed: 986 average time/residue: 0.4615 time to fit residues: 809.1984 Evaluate side-chains 855 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 588 time to evaluate : 4.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 10 SER Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain U residue 34 MET Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 38 THR Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 38 THR Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 38 THR Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 240 SER Chi-restraints excluded: chain F residue 245 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 10 SER Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 99 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 10 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 105 PHE Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 10 SER Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 38 THR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 105 PHE Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 38 THR Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 10 SER Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 147 ASN Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 227 ASN Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 141 HIS Chi-restraints excluded: chain N residue 147 ASN Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 38 THR Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 195 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 10 SER Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 10 SER Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain Q residue 214 THR Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 38 THR Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 147 ASN Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 10 SER Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 47 LYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 99 LEU Chi-restraints excluded: chain S residue 105 PHE Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 10 SER Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 38 THR Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 34 MET Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 7 SER Chi-restraints excluded: chain Z residue 81 LEU Chi-restraints excluded: chain Z residue 83 MET Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain b residue 52 TYR Chi-restraints excluded: chain c residue 52 TYR Chi-restraints excluded: chain d residue 5 VAL Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 7 SER Chi-restraints excluded: chain e residue 58 THR Chi-restraints excluded: chain e residue 81 LEU Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain h residue 52 TYR Chi-restraints excluded: chain i residue 52 TYR Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 34 MET Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 7 SER Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 34 MET Chi-restraints excluded: chain n residue 90 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 563 optimal weight: 20.0000 chunk 384 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 503 optimal weight: 7.9990 chunk 279 optimal weight: 1.9990 chunk 577 optimal weight: 20.0000 chunk 467 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 345 optimal weight: 0.0980 chunk 607 optimal weight: 8.9990 chunk 170 optimal weight: 0.7980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 ASN D 147 ASN E 147 ASN F 238 GLN G 6 ASN G 147 ASN H 6 ASN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 ASN I 147 ASN J 147 ASN K 147 ASN M 147 ASN M 227 ASN O 6 ASN O 147 ASN P 147 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 6 ASN T 147 ASN a 59 HIS b 59 HIS c 59 HIS ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 56600 Z= 0.179 Angle : 0.577 10.958 76620 Z= 0.299 Chirality : 0.037 0.175 8740 Planarity : 0.003 0.037 9540 Dihedral : 4.181 18.815 7620 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 3.19 % Allowed : 21.88 % Favored : 74.93 % 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: 2.05 (0.10), residues: 6820 helix: 2.29 (0.08), residues: 3920 sheet: 1.19 (0.14), residues: 1100 loop : -0.66 (0.15), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Z 47 HIS 0.003 0.000 HIS b 33 PHE 0.029 0.002 PHE H 105 TYR 0.013 0.001 TYR c 95 ARG 0.008 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 917 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 725 time to evaluate : 4.628 Fit side-chains revert: symmetry clash REVERT: U 109 THR cc_start: 0.2690 (p) cc_final: 0.2445 (p) REVERT: B 244 MET cc_start: 0.8279 (tpt) cc_final: 0.7745 (tpp) REVERT: C 6 ASN cc_start: 0.4889 (t160) cc_final: 0.4318 (p0) REVERT: C 244 MET cc_start: 0.7661 (tpt) cc_final: 0.7190 (tpp) REVERT: C 273 LYS cc_start: 0.8487 (ptmt) cc_final: 0.8209 (mttt) REVERT: D 238 GLN cc_start: 0.7974 (tt0) cc_final: 0.7678 (tt0) REVERT: D 244 MET cc_start: 0.8205 (tpt) cc_final: 0.7675 (tpp) REVERT: E 244 MET cc_start: 0.7766 (tpp) cc_final: 0.7483 (tpp) REVERT: F 238 GLN cc_start: 0.8080 (tt0) cc_final: 0.7738 (tt0) REVERT: G 104 PHE cc_start: 0.6684 (t80) cc_final: 0.6465 (t80) REVERT: G 187 MET cc_start: 0.7708 (mmm) cc_final: 0.7397 (mmm) REVERT: G 244 MET cc_start: 0.7808 (tpt) cc_final: 0.7275 (tpp) REVERT: H 244 MET cc_start: 0.8197 (tpt) cc_final: 0.7853 (tpp) REVERT: I 244 MET cc_start: 0.8101 (tpt) cc_final: 0.7630 (tpp) REVERT: J 238 GLN cc_start: 0.7991 (tt0) cc_final: 0.7692 (tt0) REVERT: J 244 MET cc_start: 0.7761 (tpt) cc_final: 0.7344 (tpp) REVERT: K 238 GLN cc_start: 0.8037 (tt0) cc_final: 0.7704 (tt0) REVERT: L 104 PHE cc_start: 0.6714 (t80) cc_final: 0.6437 (t80) REVERT: L 244 MET cc_start: 0.8061 (tpt) cc_final: 0.7513 (tpp) REVERT: M 104 PHE cc_start: 0.6567 (t80) cc_final: 0.6305 (t80) REVERT: M 238 GLN cc_start: 0.8006 (tt0) cc_final: 0.7788 (tt0) REVERT: P 238 GLN cc_start: 0.8012 (tt0) cc_final: 0.7760 (tt0) REVERT: Q 104 PHE cc_start: 0.6574 (t80) cc_final: 0.6324 (t80) REVERT: Q 238 GLN cc_start: 0.7857 (tt0) cc_final: 0.7572 (tt0) REVERT: R 6 ASN cc_start: 0.4482 (t160) cc_final: 0.4266 (p0) REVERT: R 244 MET cc_start: 0.7555 (tpp) cc_final: 0.7051 (tpp) REVERT: S 104 PHE cc_start: 0.6725 (t80) cc_final: 0.6492 (t80) REVERT: S 105 PHE cc_start: 0.8232 (t80) cc_final: 0.7988 (t80) REVERT: S 244 MET cc_start: 0.7464 (tpt) cc_final: 0.7216 (tpp) REVERT: T 95 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6608 (mp) REVERT: T 244 MET cc_start: 0.7618 (tpt) cc_final: 0.7260 (tpp) REVERT: V 34 MET cc_start: 0.3857 (mmm) cc_final: 0.3479 (mmm) REVERT: W 34 MET cc_start: 0.3788 (mtt) cc_final: 0.3487 (mtt) REVERT: W 107 GLN cc_start: 0.5876 (tm-30) cc_final: 0.4677 (pm20) REVERT: X 58 THR cc_start: 0.5394 (t) cc_final: 0.5080 (p) REVERT: Y 34 MET cc_start: 0.3982 (OUTLIER) cc_final: 0.3696 (mmm) REVERT: g 34 MET cc_start: 0.5655 (mmm) cc_final: 0.5376 (mmm) REVERT: h 107 GLN cc_start: 0.5268 (tm-30) cc_final: 0.4680 (pm20) REVERT: i 107 GLN cc_start: 0.5611 (tm-30) cc_final: 0.4625 (pm20) REVERT: j 34 MET cc_start: 0.3567 (OUTLIER) cc_final: 0.3151 (mmm) REVERT: k 34 MET cc_start: 0.3668 (mmm) cc_final: 0.3304 (mmm) REVERT: n 34 MET cc_start: 0.3616 (OUTLIER) cc_final: 0.3288 (mmm) outliers start: 192 outliers final: 130 residues processed: 878 average time/residue: 0.4678 time to fit residues: 721.0307 Evaluate side-chains 747 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 613 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 180 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 180 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 95 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 34 MET Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 83 MET Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 70 ILE Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain g residue 90 ASP Chi-restraints excluded: chain h residue 12 VAL Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 34 MET Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 90 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 227 optimal weight: 2.9990 chunk 609 optimal weight: 30.0000 chunk 133 optimal weight: 3.9990 chunk 397 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 677 optimal weight: 20.0000 chunk 562 optimal weight: 10.0000 chunk 313 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 224 optimal weight: 3.9990 chunk 355 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 GLN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 147 ASN L 6 ASN M 6 ASN M 227 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 ASN ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 56600 Z= 0.207 Angle : 0.585 8.791 76620 Z= 0.302 Chirality : 0.037 0.187 8740 Planarity : 0.003 0.038 9540 Dihedral : 4.156 18.782 7620 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.04 % Allowed : 21.78 % Favored : 74.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.10), residues: 6820 helix: 2.31 (0.08), residues: 3940 sheet: 1.16 (0.14), residues: 1100 loop : -0.69 (0.16), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP S 221 HIS 0.005 0.001 HIS b 33 PHE 0.031 0.002 PHE F 105 TYR 0.012 0.001 TYR S 220 ARG 0.008 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 921 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 678 time to evaluate : 4.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8711 (tm) REVERT: B 244 MET cc_start: 0.8250 (tpt) cc_final: 0.7735 (tpp) REVERT: C 6 ASN cc_start: 0.4907 (t160) cc_final: 0.4247 (p0) REVERT: C 244 MET cc_start: 0.7737 (tpt) cc_final: 0.7214 (tpp) REVERT: C 273 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8200 (mttt) REVERT: C 274 ASP cc_start: 0.8345 (p0) cc_final: 0.7902 (p0) REVERT: D 238 GLN cc_start: 0.8005 (tt0) cc_final: 0.7697 (tt0) REVERT: D 244 MET cc_start: 0.8294 (tpt) cc_final: 0.7675 (tpp) REVERT: E 244 MET cc_start: 0.7789 (tpp) cc_final: 0.7496 (tpp) REVERT: F 238 GLN cc_start: 0.7964 (tt0) cc_final: 0.7640 (tt0) REVERT: G 22 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8704 (tm) REVERT: G 104 PHE cc_start: 0.6726 (t80) cc_final: 0.6457 (t80) REVERT: G 187 MET cc_start: 0.7684 (mmm) cc_final: 0.7434 (mmm) REVERT: G 244 MET cc_start: 0.7858 (tpt) cc_final: 0.7273 (tpp) REVERT: H 244 MET cc_start: 0.8202 (tpt) cc_final: 0.7875 (tpp) REVERT: I 104 PHE cc_start: 0.6670 (t80) cc_final: 0.6443 (t80) REVERT: I 244 MET cc_start: 0.8133 (tpt) cc_final: 0.7594 (tpp) REVERT: J 22 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8717 (tm) REVERT: J 238 GLN cc_start: 0.8014 (tt0) cc_final: 0.7694 (tt0) REVERT: J 244 MET cc_start: 0.7795 (tpt) cc_final: 0.7308 (tpp) REVERT: K 104 PHE cc_start: 0.6653 (t80) cc_final: 0.6409 (t80) REVERT: K 238 GLN cc_start: 0.8052 (tt0) cc_final: 0.7728 (tt0) REVERT: L 22 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8692 (tm) REVERT: L 104 PHE cc_start: 0.6726 (t80) cc_final: 0.6512 (t80) REVERT: L 244 MET cc_start: 0.8095 (tpt) cc_final: 0.7572 (tpp) REVERT: M 104 PHE cc_start: 0.6601 (t80) cc_final: 0.6343 (t80) REVERT: M 238 GLN cc_start: 0.8033 (tt0) cc_final: 0.7793 (tt0) REVERT: N 244 MET cc_start: 0.8097 (tpp) cc_final: 0.7207 (tpp) REVERT: O 22 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8730 (tm) REVERT: P 238 GLN cc_start: 0.8032 (tt0) cc_final: 0.7790 (tt0) REVERT: Q 22 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8669 (tm) REVERT: Q 104 PHE cc_start: 0.6631 (t80) cc_final: 0.6388 (t80) REVERT: Q 238 GLN cc_start: 0.7859 (tt0) cc_final: 0.7592 (tt0) REVERT: S 105 PHE cc_start: 0.8264 (t80) cc_final: 0.8005 (t80) REVERT: S 244 MET cc_start: 0.7527 (tpt) cc_final: 0.7103 (tpp) REVERT: T 22 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8740 (tm) REVERT: T 244 MET cc_start: 0.7718 (tpt) cc_final: 0.7266 (tpp) REVERT: V 34 MET cc_start: 0.3983 (OUTLIER) cc_final: 0.3616 (mmm) REVERT: W 107 GLN cc_start: 0.6035 (tm-30) cc_final: 0.5182 (pm20) REVERT: X 58 THR cc_start: 0.5363 (t) cc_final: 0.5096 (p) REVERT: Y 34 MET cc_start: 0.4160 (OUTLIER) cc_final: 0.3893 (mmm) REVERT: a 83 MET cc_start: 0.6141 (ptp) cc_final: 0.5769 (ptp) REVERT: g 34 MET cc_start: 0.5817 (mmm) cc_final: 0.5541 (mmm) REVERT: g 83 MET cc_start: 0.7564 (ptp) cc_final: 0.7322 (ptp) REVERT: i 107 GLN cc_start: 0.5720 (tm-30) cc_final: 0.4683 (pm20) REVERT: j 34 MET cc_start: 0.3686 (OUTLIER) cc_final: 0.3302 (mmm) REVERT: k 34 MET cc_start: 0.3809 (mmm) cc_final: 0.3455 (mmm) REVERT: n 34 MET cc_start: 0.3783 (OUTLIER) cc_final: 0.3469 (mmm) outliers start: 243 outliers final: 188 residues processed: 871 average time/residue: 0.4576 time to fit residues: 703.2197 Evaluate side-chains 825 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 625 time to evaluate : 4.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 227 ASN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 34 MET Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 81 LEU Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 34 MET Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 83 MET Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain c residue 98 VAL Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain h residue 52 TYR Chi-restraints excluded: chain i residue 34 MET Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 34 MET Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 81 LEU Chi-restraints excluded: chain n residue 90 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 652 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 385 optimal weight: 10.0000 chunk 494 optimal weight: 0.5980 chunk 383 optimal weight: 0.9990 chunk 570 optimal weight: 30.0000 chunk 378 optimal weight: 0.7980 chunk 674 optimal weight: 3.9990 chunk 422 optimal weight: 4.9990 chunk 411 optimal weight: 4.9990 chunk 311 optimal weight: 9.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 HIS F 6 ASN F 147 ASN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 181 HIS M 227 ASN N 147 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS ** b 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 56600 Z= 0.172 Angle : 0.571 9.103 76620 Z= 0.293 Chirality : 0.037 0.169 8740 Planarity : 0.003 0.039 9540 Dihedral : 4.089 18.220 7620 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.52 % Allowed : 22.38 % Favored : 74.10 % 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: 2.06 (0.10), residues: 6820 helix: 2.28 (0.08), residues: 4020 sheet: 1.14 (0.14), residues: 1100 loop : -0.76 (0.16), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 221 HIS 0.004 0.000 HIS a 33 PHE 0.027 0.002 PHE G 105 TYR 0.011 0.001 TYR j 52 ARG 0.008 0.000 ARG B 241 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 920 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 708 time to evaluate : 4.504 Fit side-chains revert: symmetry clash REVERT: B 244 MET cc_start: 0.8226 (tpt) cc_final: 0.7736 (tpp) REVERT: C 6 ASN cc_start: 0.4893 (t160) cc_final: 0.4232 (p0) REVERT: C 244 MET cc_start: 0.7679 (tpt) cc_final: 0.7180 (tpp) REVERT: C 273 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8169 (mttt) REVERT: C 274 ASP cc_start: 0.8327 (p0) cc_final: 0.7837 (p0) REVERT: D 244 MET cc_start: 0.8301 (tpt) cc_final: 0.7666 (tpp) REVERT: E 22 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8673 (tm) REVERT: E 244 MET cc_start: 0.7753 (tpp) cc_final: 0.7490 (tpp) REVERT: F 99 LEU cc_start: 0.7591 (mt) cc_final: 0.6954 (mp) REVERT: F 238 GLN cc_start: 0.7913 (tt0) cc_final: 0.7559 (tt0) REVERT: G 187 MET cc_start: 0.7647 (mmm) cc_final: 0.7396 (mmm) REVERT: G 244 MET cc_start: 0.7845 (tpt) cc_final: 0.7293 (tpp) REVERT: H 244 MET cc_start: 0.8190 (tpt) cc_final: 0.7868 (tpp) REVERT: I 104 PHE cc_start: 0.6581 (t80) cc_final: 0.6356 (t80) REVERT: I 244 MET cc_start: 0.8173 (tpt) cc_final: 0.7634 (tpp) REVERT: J 22 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8697 (tm) REVERT: J 238 GLN cc_start: 0.7981 (tt0) cc_final: 0.7618 (tt0) REVERT: J 244 MET cc_start: 0.7742 (tpt) cc_final: 0.7312 (tpp) REVERT: L 22 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8732 (tm) REVERT: L 104 PHE cc_start: 0.6611 (t80) cc_final: 0.6342 (t80) REVERT: L 244 MET cc_start: 0.8105 (tpt) cc_final: 0.7600 (tpp) REVERT: M 104 PHE cc_start: 0.6547 (t80) cc_final: 0.6279 (t80) REVERT: M 238 GLN cc_start: 0.7975 (tt0) cc_final: 0.7765 (tt0) REVERT: O 22 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8712 (tm) REVERT: P 238 GLN cc_start: 0.7988 (tt0) cc_final: 0.7732 (tt0) REVERT: Q 22 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8738 (tm) REVERT: Q 104 PHE cc_start: 0.6542 (t80) cc_final: 0.6278 (t80) REVERT: Q 238 GLN cc_start: 0.7831 (tt0) cc_final: 0.7552 (tt0) REVERT: S 230 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7768 (tm-30) REVERT: S 244 MET cc_start: 0.7443 (tpt) cc_final: 0.7081 (tpp) REVERT: T 244 MET cc_start: 0.7658 (tpt) cc_final: 0.7232 (tpp) REVERT: W 107 GLN cc_start: 0.6015 (tm-30) cc_final: 0.5150 (pm20) REVERT: a 11 LEU cc_start: 0.5802 (OUTLIER) cc_final: 0.5223 (pt) REVERT: c 34 MET cc_start: 0.6321 (mmp) cc_final: 0.5937 (ttt) REVERT: g 34 MET cc_start: 0.5876 (mmm) cc_final: 0.5545 (mmm) REVERT: i 107 GLN cc_start: 0.5761 (tm-30) cc_final: 0.4722 (pm20) REVERT: k 34 MET cc_start: 0.3880 (mmm) cc_final: 0.3528 (mmm) outliers start: 212 outliers final: 168 residues processed: 865 average time/residue: 0.4568 time to fit residues: 695.4736 Evaluate side-chains 827 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 652 time to evaluate : 4.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 245 MET Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 213 LEU Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 227 ASN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 52 TYR Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 81 LEU Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 58 THR Chi-restraints excluded: chain Z residue 83 MET Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain a residue 11 LEU Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain h residue 52 TYR Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain m residue 81 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 81 LEU Chi-restraints excluded: chain n residue 90 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 417 optimal weight: 3.9990 chunk 269 optimal weight: 30.0000 chunk 402 optimal weight: 6.9990 chunk 203 optimal weight: 0.3980 chunk 132 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 428 optimal weight: 4.9990 chunk 459 optimal weight: 4.9990 chunk 333 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 530 optimal weight: 20.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 39 GLN ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 HIS ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 39 GLN ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 39 GLN a 59 HIS b 39 GLN ** b 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 39 GLN f 39 GLN ** f 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 39 GLN m 39 GLN m 59 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 56600 Z= 0.304 Angle : 0.654 9.828 76620 Z= 0.341 Chirality : 0.040 0.202 8740 Planarity : 0.004 0.042 9540 Dihedral : 4.397 19.806 7620 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 4.72 % Allowed : 21.73 % Favored : 73.55 % 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: 1.86 (0.10), residues: 6820 helix: 2.17 (0.08), residues: 3880 sheet: 1.06 (0.14), residues: 1100 loop : -0.72 (0.16), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 221 HIS 0.004 0.001 HIS l 33 PHE 0.029 0.003 PHE Q 160 TYR 0.017 0.002 TYR f 95 ARG 0.008 0.000 ARG Q 241 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 643 time to evaluate : 4.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8669 (tm) REVERT: C 6 ASN cc_start: 0.5062 (t160) cc_final: 0.4303 (p0) REVERT: C 244 MET cc_start: 0.7880 (tpt) cc_final: 0.7253 (tpp) REVERT: C 273 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8263 (mttt) REVERT: E 22 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8739 (tm) REVERT: E 244 MET cc_start: 0.7845 (tpp) cc_final: 0.7554 (tpp) REVERT: G 22 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8680 (tm) REVERT: G 104 PHE cc_start: 0.6735 (t80) cc_final: 0.6509 (t80) REVERT: G 244 MET cc_start: 0.8022 (tpt) cc_final: 0.7330 (tpp) REVERT: H 244 MET cc_start: 0.8184 (tpt) cc_final: 0.7884 (tpp) REVERT: I 244 MET cc_start: 0.8256 (tpt) cc_final: 0.7709 (tpp) REVERT: J 22 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8755 (tm) REVERT: J 238 GLN cc_start: 0.8024 (tt0) cc_final: 0.7723 (tt0) REVERT: J 244 MET cc_start: 0.7882 (tpt) cc_final: 0.7301 (tpp) REVERT: L 6 ASN cc_start: 0.4385 (t0) cc_final: 0.4147 (p0) REVERT: L 22 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8653 (tm) REVERT: L 104 PHE cc_start: 0.6876 (t80) cc_final: 0.6615 (t80) REVERT: L 244 MET cc_start: 0.8189 (tpt) cc_final: 0.7700 (tpp) REVERT: M 238 GLN cc_start: 0.8094 (tt0) cc_final: 0.7874 (tt0) REVERT: N 244 MET cc_start: 0.7910 (tpp) cc_final: 0.7295 (tpp) REVERT: N 245 MET cc_start: 0.8043 (mmm) cc_final: 0.7693 (tpp) REVERT: O 22 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8749 (tm) REVERT: P 238 GLN cc_start: 0.8087 (tt0) cc_final: 0.7828 (tt0) REVERT: Q 22 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8679 (tm) REVERT: Q 238 GLN cc_start: 0.7894 (tt0) cc_final: 0.7657 (tt0) REVERT: S 230 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7806 (tm-30) REVERT: S 244 MET cc_start: 0.7733 (tpt) cc_final: 0.7203 (tpp) REVERT: T 22 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8752 (tm) REVERT: T 244 MET cc_start: 0.7841 (tpt) cc_final: 0.7296 (tpp) REVERT: X 36 TRP cc_start: 0.5631 (t-100) cc_final: 0.5307 (t-100) REVERT: b 34 MET cc_start: 0.6483 (mmp) cc_final: 0.5786 (tpp) REVERT: c 34 MET cc_start: 0.6258 (mmp) cc_final: 0.5981 (ttt) REVERT: d 83 MET cc_start: 0.6579 (OUTLIER) cc_final: 0.5737 (ptm) REVERT: g 34 MET cc_start: 0.6177 (mmm) cc_final: 0.5875 (mmm) REVERT: i 107 GLN cc_start: 0.5732 (tm-30) cc_final: 0.4632 (pm20) REVERT: j 34 MET cc_start: 0.4029 (OUTLIER) cc_final: 0.3698 (mmm) outliers start: 284 outliers final: 241 residues processed: 848 average time/residue: 0.4573 time to fit residues: 686.5986 Evaluate side-chains 850 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 598 time to evaluate : 5.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 245 MET Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 187 MET Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 227 ASN Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 213 LEU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 43 CYS Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 188 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 175 ASP Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 43 CYS Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 188 LEU Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 52 TYR Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 52 TYR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 81 LEU Chi-restraints excluded: chain X residue 34 MET Chi-restraints excluded: chain X residue 52 TYR Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 52 TYR Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain a residue 7 SER Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain b residue 52 TYR Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain c residue 52 TYR Chi-restraints excluded: chain d residue 34 MET Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 83 MET Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 98 VAL Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain h residue 34 MET Chi-restraints excluded: chain h residue 52 TYR Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain i residue 34 MET Chi-restraints excluded: chain i residue 52 TYR Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 52 TYR Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 52 TYR Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 81 LEU Chi-restraints excluded: chain n residue 90 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 613 optimal weight: 20.0000 chunk 646 optimal weight: 40.0000 chunk 589 optimal weight: 9.9990 chunk 628 optimal weight: 10.0000 chunk 378 optimal weight: 1.9990 chunk 273 optimal weight: 2.9990 chunk 493 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 568 optimal weight: 20.0000 chunk 594 optimal weight: 9.9990 chunk 626 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 ASN C 6 ASN ** C 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 238 GLN ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 ASN ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS g 39 GLN ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 56600 Z= 0.387 Angle : 0.711 9.283 76620 Z= 0.372 Chirality : 0.043 0.233 8740 Planarity : 0.004 0.045 9540 Dihedral : 4.749 21.989 7620 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 5.22 % Allowed : 21.71 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.10), residues: 6820 helix: 1.78 (0.08), residues: 3880 sheet: 0.84 (0.16), residues: 880 loop : -0.98 (0.14), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP V 36 HIS 0.006 0.001 HIS l 33 PHE 0.029 0.003 PHE Q 160 TYR 0.024 0.002 TYR V 95 ARG 0.009 0.001 ARG m 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 939 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 314 poor density : 625 time to evaluate : 4.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 83 MET cc_start: 0.6251 (ptt) cc_final: 0.6050 (ptt) REVERT: B 22 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8682 (tm) REVERT: C 6 ASN cc_start: 0.5057 (t0) cc_final: 0.4428 (p0) REVERT: C 244 MET cc_start: 0.7975 (tpt) cc_final: 0.7660 (tpp) REVERT: C 273 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8289 (mttt) REVERT: D 104 PHE cc_start: 0.6995 (t80) cc_final: 0.6736 (t80) REVERT: E 22 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8787 (tm) REVERT: E 244 MET cc_start: 0.7886 (tpp) cc_final: 0.7623 (tpp) REVERT: G 22 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8685 (tm) REVERT: G 244 MET cc_start: 0.8116 (tpt) cc_final: 0.7371 (tpp) REVERT: H 244 MET cc_start: 0.8204 (tpt) cc_final: 0.7900 (tpp) REVERT: I 104 PHE cc_start: 0.6963 (t80) cc_final: 0.6714 (t80) REVERT: I 244 MET cc_start: 0.8280 (tpt) cc_final: 0.7946 (tpp) REVERT: J 22 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8795 (tm) REVERT: J 244 MET cc_start: 0.7969 (tpt) cc_final: 0.7345 (tpp) REVERT: L 22 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8677 (tm) REVERT: L 104 PHE cc_start: 0.6956 (t80) cc_final: 0.6744 (t80) REVERT: L 105 PHE cc_start: 0.8237 (t80) cc_final: 0.8002 (t80) REVERT: L 244 MET cc_start: 0.8199 (tpt) cc_final: 0.7727 (tpp) REVERT: M 238 GLN cc_start: 0.8143 (tt0) cc_final: 0.7910 (tt0) REVERT: N 244 MET cc_start: 0.7850 (tpp) cc_final: 0.7194 (tpp) REVERT: N 245 MET cc_start: 0.7986 (mmm) cc_final: 0.7670 (tpp) REVERT: O 22 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8804 (tm) REVERT: O 230 GLU cc_start: 0.8076 (tt0) cc_final: 0.7794 (tm-30) REVERT: O 241 ARG cc_start: 0.7818 (ttt180) cc_final: 0.7593 (ttp80) REVERT: P 238 GLN cc_start: 0.8101 (tt0) cc_final: 0.7839 (tt0) REVERT: Q 22 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8682 (tm) REVERT: Q 105 PHE cc_start: 0.8260 (t80) cc_final: 0.8026 (t80) REVERT: Q 238 GLN cc_start: 0.7977 (tt0) cc_final: 0.7725 (tt0) REVERT: S 230 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7844 (tm-30) REVERT: S 244 MET cc_start: 0.7754 (tpt) cc_final: 0.7201 (tpp) REVERT: T 22 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8791 (tm) REVERT: T 244 MET cc_start: 0.7911 (tpt) cc_final: 0.7309 (tpp) REVERT: W 34 MET cc_start: 0.6322 (mmp) cc_final: 0.5796 (ttt) REVERT: X 109 THR cc_start: 0.2929 (p) cc_final: 0.2669 (p) REVERT: c 34 MET cc_start: 0.6302 (mmp) cc_final: 0.5952 (ttt) REVERT: g 34 MET cc_start: 0.6481 (mmm) cc_final: 0.6220 (mmm) REVERT: i 109 THR cc_start: 0.3025 (p) cc_final: 0.2785 (p) REVERT: j 34 MET cc_start: 0.4374 (OUTLIER) cc_final: 0.4075 (mmm) REVERT: k 83 MET cc_start: 0.6124 (OUTLIER) cc_final: 0.5701 (ptt) outliers start: 314 outliers final: 279 residues processed: 844 average time/residue: 0.4670 time to fit residues: 690.2539 Evaluate side-chains 880 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 590 time to evaluate : 4.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 187 MET Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 43 CYS Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 175 ASP Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 175 ASP Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 108 THR Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 187 MET Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 43 CYS Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 206 VAL Chi-restraints excluded: chain G residue 245 MET Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 175 ASP Chi-restraints excluded: chain H residue 187 MET Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 9 VAL Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 175 ASP Chi-restraints excluded: chain I residue 187 MET Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 43 CYS Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 112 VAL Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 175 ASP Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain J residue 264 ILE Chi-restraints excluded: chain K residue 9 VAL Chi-restraints excluded: chain K residue 43 CYS Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 187 MET Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain L residue 9 VAL Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 108 THR Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 175 ASP Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain M residue 9 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 227 ASN Chi-restraints excluded: chain N residue 38 THR Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 206 VAL Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 9 VAL Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 43 CYS Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 108 THR Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 175 ASP Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 43 CYS Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 175 ASP Chi-restraints excluded: chain P residue 187 MET Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 38 THR Chi-restraints excluded: chain Q residue 43 CYS Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 108 THR Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 175 ASP Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain R residue 9 VAL Chi-restraints excluded: chain R residue 10 SER Chi-restraints excluded: chain R residue 43 CYS Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 175 ASP Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 187 MET Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 23 ILE Chi-restraints excluded: chain S residue 43 CYS Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 175 ASP Chi-restraints excluded: chain S residue 187 MET Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 9 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 43 CYS Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 175 ASP Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 52 TYR Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 52 TYR Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 81 LEU Chi-restraints excluded: chain X residue 52 TYR Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 52 TYR Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain a residue 52 TYR Chi-restraints excluded: chain a residue 83 MET Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain b residue 52 TYR Chi-restraints excluded: chain b residue 68 PHE Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain c residue 52 TYR Chi-restraints excluded: chain d residue 34 MET Chi-restraints excluded: chain d residue 52 TYR Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain e residue 98 VAL Chi-restraints excluded: chain f residue 34 MET Chi-restraints excluded: chain f residue 52 TYR Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 5 VAL Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain h residue 52 TYR Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain i residue 52 TYR Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 34 MET Chi-restraints excluded: chain j residue 52 TYR Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 83 MET Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 52 TYR Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 81 LEU Chi-restraints excluded: chain n residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 412 optimal weight: 10.0000 chunk 664 optimal weight: 30.0000 chunk 405 optimal weight: 0.1980 chunk 315 optimal weight: 1.9990 chunk 462 optimal weight: 0.9980 chunk 697 optimal weight: 10.0000 chunk 641 optimal weight: 20.0000 chunk 555 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 428 optimal weight: 0.9990 chunk 340 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 147 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 227 ASN ** P 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 59 HIS ** n 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 56600 Z= 0.180 Angle : 0.607 9.700 76620 Z= 0.311 Chirality : 0.038 0.195 8740 Planarity : 0.004 0.046 9540 Dihedral : 4.420 20.031 7620 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.17 % Allowed : 23.75 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.10), residues: 6820 helix: 2.21 (0.08), residues: 3900 sheet: 0.86 (0.15), residues: 1000 loop : -0.90 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP h 36 HIS 0.004 0.000 HIS h 33 PHE 0.030 0.002 PHE G 105 TYR 0.016 0.001 TYR i 95 ARG 0.010 0.000 ARG H 241 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13640 Ramachandran restraints generated. 6820 Oldfield, 0 Emsley, 6820 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 884 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 693 time to evaluate : 4.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8666 (tm) REVERT: C 6 ASN cc_start: 0.4868 (t0) cc_final: 0.4371 (p0) REVERT: C 244 MET cc_start: 0.7789 (tpt) cc_final: 0.7271 (tpp) REVERT: C 273 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8203 (mttt) REVERT: D 244 MET cc_start: 0.8331 (tpt) cc_final: 0.8017 (tpp) REVERT: E 22 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8739 (tm) REVERT: G 22 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8682 (tm) REVERT: G 244 MET cc_start: 0.7956 (tpt) cc_final: 0.7391 (tpp) REVERT: H 244 MET cc_start: 0.8176 (tpt) cc_final: 0.7912 (tpp) REVERT: I 220 TYR cc_start: 0.8840 (t80) cc_final: 0.8614 (t80) REVERT: I 244 MET cc_start: 0.8201 (tpt) cc_final: 0.7927 (tpp) REVERT: J 244 MET cc_start: 0.7797 (tpt) cc_final: 0.7406 (tpp) REVERT: L 104 PHE cc_start: 0.6719 (t80) cc_final: 0.6515 (t80) REVERT: L 244 MET cc_start: 0.8112 (tpt) cc_final: 0.7646 (tpp) REVERT: M 238 GLN cc_start: 0.8003 (tt0) cc_final: 0.7752 (tt0) REVERT: M 244 MET cc_start: 0.8162 (tpt) cc_final: 0.7764 (tpp) REVERT: N 244 MET cc_start: 0.7823 (tpp) cc_final: 0.7290 (tpp) REVERT: N 245 MET cc_start: 0.7970 (mmm) cc_final: 0.7619 (tpp) REVERT: O 244 MET cc_start: 0.8315 (tpt) cc_final: 0.8094 (tpp) REVERT: P 238 GLN cc_start: 0.7980 (tt0) cc_final: 0.7707 (tt0) REVERT: P 241 ARG cc_start: 0.7958 (ttt90) cc_final: 0.7627 (tpt170) REVERT: Q 238 GLN cc_start: 0.7847 (tt0) cc_final: 0.7584 (tt0) REVERT: S 244 MET cc_start: 0.7598 (tpt) cc_final: 0.7204 (tpp) REVERT: T 22 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8736 (tm) REVERT: T 244 MET cc_start: 0.7753 (tpt) cc_final: 0.7366 (tpp) REVERT: V 34 MET cc_start: 0.6791 (mmp) cc_final: 0.6549 (tmm) REVERT: W 34 MET cc_start: 0.5929 (mmp) cc_final: 0.5617 (ttt) REVERT: X 109 THR cc_start: 0.2657 (p) cc_final: 0.2400 (p) REVERT: b 34 MET cc_start: 0.6038 (mmp) cc_final: 0.5219 (ttm) REVERT: c 34 MET cc_start: 0.6378 (mmp) cc_final: 0.6129 (ttt) REVERT: d 83 MET cc_start: 0.6635 (ptm) cc_final: 0.6125 (ppp) REVERT: g 34 MET cc_start: 0.6361 (mmm) cc_final: 0.6149 (mmm) REVERT: i 36 TRP cc_start: 0.5788 (t-100) cc_final: 0.5231 (t-100) REVERT: m 34 MET cc_start: 0.7285 (mmp) cc_final: 0.7075 (mmp) outliers start: 191 outliers final: 177 residues processed: 836 average time/residue: 0.4652 time to fit residues: 676.5806 Evaluate side-chains 834 residues out of total 6020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 652 time to evaluate : 4.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 CYS Chi-restraints excluded: chain A residue 57 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain U residue 52 TYR Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain C residue 43 CYS Chi-restraints excluded: chain C residue 57 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain C residue 245 MET Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 214 THR Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 43 CYS Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 198 ILE Chi-restraints excluded: chain E residue 245 MET Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain F residue 43 CYS Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 198 ILE Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 43 CYS Chi-restraints excluded: chain G residue 57 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 188 LEU Chi-restraints excluded: chain G residue 192 LEU Chi-restraints excluded: chain G residue 245 MET Chi-restraints excluded: chain G residue 274 ASP Chi-restraints excluded: chain H residue 43 CYS Chi-restraints excluded: chain H residue 47 LYS Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 192 LEU Chi-restraints excluded: chain H residue 206 VAL Chi-restraints excluded: chain H residue 264 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 47 LYS Chi-restraints excluded: chain I residue 57 VAL Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 192 LEU Chi-restraints excluded: chain I residue 206 VAL Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 264 ILE Chi-restraints excluded: chain J residue 47 LYS Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 108 THR Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 192 LEU Chi-restraints excluded: chain J residue 206 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 108 THR Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 192 LEU Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 264 ILE Chi-restraints excluded: chain L residue 43 CYS Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 180 LEU Chi-restraints excluded: chain L residue 192 LEU Chi-restraints excluded: chain L residue 206 VAL Chi-restraints excluded: chain L residue 231 LEU Chi-restraints excluded: chain M residue 47 LYS Chi-restraints excluded: chain M residue 57 VAL Chi-restraints excluded: chain M residue 108 THR Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 192 LEU Chi-restraints excluded: chain M residue 206 VAL Chi-restraints excluded: chain M residue 227 ASN Chi-restraints excluded: chain N residue 57 VAL Chi-restraints excluded: chain N residue 108 THR Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 192 LEU Chi-restraints excluded: chain N residue 214 THR Chi-restraints excluded: chain O residue 47 LYS Chi-restraints excluded: chain O residue 57 VAL Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 192 LEU Chi-restraints excluded: chain O residue 206 VAL Chi-restraints excluded: chain O residue 245 MET Chi-restraints excluded: chain P residue 43 CYS Chi-restraints excluded: chain P residue 47 LYS Chi-restraints excluded: chain P residue 57 VAL Chi-restraints excluded: chain P residue 108 THR Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 192 LEU Chi-restraints excluded: chain P residue 206 VAL Chi-restraints excluded: chain P residue 214 THR Chi-restraints excluded: chain P residue 264 ILE Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 188 LEU Chi-restraints excluded: chain Q residue 192 LEU Chi-restraints excluded: chain Q residue 206 VAL Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 180 LEU Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 264 ILE Chi-restraints excluded: chain S residue 57 VAL Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 192 LEU Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 206 VAL Chi-restraints excluded: chain S residue 214 THR Chi-restraints excluded: chain S residue 264 ILE Chi-restraints excluded: chain S residue 274 ASP Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 47 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 108 THR Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 171 ILE Chi-restraints excluded: chain T residue 192 LEU Chi-restraints excluded: chain T residue 206 VAL Chi-restraints excluded: chain T residue 264 ILE Chi-restraints excluded: chain T residue 274 ASP Chi-restraints excluded: chain V residue 58 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 81 LEU Chi-restraints excluded: chain X residue 81 LEU Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 58 THR Chi-restraints excluded: chain Y residue 81 LEU Chi-restraints excluded: chain Y residue 90 ASP Chi-restraints excluded: chain Z residue 98 VAL Chi-restraints excluded: chain a residue 90 ASP Chi-restraints excluded: chain b residue 81 LEU Chi-restraints excluded: chain b residue 90 ASP Chi-restraints excluded: chain d residue 81 LEU Chi-restraints excluded: chain d residue 90 ASP Chi-restraints excluded: chain f residue 58 THR Chi-restraints excluded: chain f residue 81 LEU Chi-restraints excluded: chain f residue 90 ASP Chi-restraints excluded: chain g residue 52 TYR Chi-restraints excluded: chain h residue 52 TYR Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain i residue 58 THR Chi-restraints excluded: chain i residue 90 ASP Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 81 LEU Chi-restraints excluded: chain j residue 90 ASP Chi-restraints excluded: chain k residue 58 THR Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 90 ASP Chi-restraints excluded: chain l residue 58 THR Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 58 THR Chi-restraints excluded: chain n residue 81 LEU Chi-restraints excluded: chain n residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 700 random chunks: chunk 441 optimal weight: 6.9990 chunk 591 optimal weight: 20.0000 chunk 170 optimal weight: 0.9990 chunk 512 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 556 optimal weight: 30.0000 chunk 232 optimal weight: 0.0980 chunk 571 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 270 GLN ** S 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 59 HIS ** b 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.180588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.152212 restraints weight = 90165.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.150084 restraints weight = 196009.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.150756 restraints weight = 177304.824| |-----------------------------------------------------------------------------| r_work (final): 0.3937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 56600 Z= 0.176 Angle : 0.604 17.350 76620 Z= 0.308 Chirality : 0.037 0.175 8740 Planarity : 0.003 0.047 9540 Dihedral : 4.275 25.964 7620 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.24 % Allowed : 23.79 % Favored : 72.97 % 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: 1.85 (0.10), residues: 6820 helix: 2.22 (0.08), residues: 4000 sheet: 0.85 (0.15), residues: 1000 loop : -0.84 (0.15), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP Y 36 HIS 0.008 0.000 HIS f 33 PHE 0.030 0.002 PHE G 105 TYR 0.021 0.001 TYR n 94 ARG 0.010 0.000 ARG Q 241 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11670.65 seconds wall clock time: 206 minutes 51.27 seconds (12411.27 seconds total)