Starting phenix.real_space_refine on Tue Feb 20 08:34:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5n_26356/02_2024/7u5n_26356.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5n_26356/02_2024/7u5n_26356.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5n_26356/02_2024/7u5n_26356.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5n_26356/02_2024/7u5n_26356.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5n_26356/02_2024/7u5n_26356.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5n_26356/02_2024/7u5n_26356.pdb" } resolution = 2.58 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= 0.094 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: 5 Type Number sf(0) Gaussians Mn 10 7.51 5 S 220 5.16 5 C 17240 2.51 5 N 4760 2.21 5 O 5050 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 340": "NH1" <-> "NH2" Residue "B GLU 338": "OE1" <-> "OE2" Residue "B ARG 340": "NH1" <-> "NH2" Residue "C GLU 338": "OE1" <-> "OE2" Residue "C ARG 340": "NH1" <-> "NH2" Residue "D GLU 338": "OE1" <-> "OE2" Residue "D ARG 340": "NH1" <-> "NH2" Residue "E GLU 338": "OE1" <-> "OE2" Residue "E ARG 340": "NH1" <-> "NH2" Residue "F GLU 338": "OE1" <-> "OE2" Residue "F ARG 340": "NH1" <-> "NH2" Residue "G GLU 338": "OE1" <-> "OE2" Residue "G ARG 340": "NH1" <-> "NH2" Residue "H GLU 338": "OE1" <-> "OE2" Residue "H ARG 340": "NH1" <-> "NH2" Residue "I GLU 338": "OE1" <-> "OE2" Residue "I ARG 340": "NH1" <-> "NH2" Residue "J GLU 338": "OE1" <-> "OE2" Residue "J ARG 340": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27280 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2727 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 319} Chain breaks: 1 Chain: "B" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2727 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 319} Chain breaks: 1 Chain: "C" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2727 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 319} Chain breaks: 1 Chain: "D" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2727 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 319} Chain breaks: 1 Chain: "E" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2727 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 319} Chain breaks: 1 Chain: "F" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2727 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 319} Chain breaks: 1 Chain: "G" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2727 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 319} Chain breaks: 1 Chain: "H" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2727 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 319} Chain breaks: 1 Chain: "I" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2727 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 319} Chain breaks: 1 Chain: "J" Number of atoms: 2727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2727 Classifications: {'peptide': 343} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 319} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.52, per 1000 atoms: 0.53 Number of scatterers: 27280 At special positions: 0 Unit cell: (135.89, 131.61, 108.07, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 10 24.99 S 220 16.00 O 5050 8.00 N 4760 7.00 C 17240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 10.36 Conformation dependent library (CDL) restraints added in 5.1 seconds 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6220 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 20 sheets defined 37.6% alpha, 33.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.94 Creating SS restraints... Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS A 14 " --> pdb=" O ASN A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 57 Processing helix chain 'A' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 65 through 68' Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP A 289 " --> pdb=" O ILE A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 333 Processing helix chain 'A' and resid 347 through 360 Processing helix chain 'B' and resid 4 through 9 Processing helix chain 'B' and resid 10 through 19 removed outlier: 3.760A pdb=" N LYS B 14 " --> pdb=" O ASN B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 57 Processing helix chain 'B' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE B 68 " --> pdb=" O SER B 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL B 176 " --> pdb=" O GLY B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 233 removed outlier: 4.222A pdb=" N GLY B 215 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 263 Processing helix chain 'B' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.689A pdb=" N ASP B 289 " --> pdb=" O ILE B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 347 through 360 Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE C 68 " --> pdb=" O SER C 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 65 through 68' Processing helix chain 'C' and resid 113 through 124 Processing helix chain 'C' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL C 176 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 266 through 280 removed outlier: 3.740A pdb=" N LYS C 279 " --> pdb=" O GLU C 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG C 280 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP C 289 " --> pdb=" O ILE C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 333 Processing helix chain 'C' and resid 347 through 360 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS D 14 " --> pdb=" O ASN D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 57 Processing helix chain 'D' and resid 65 through 68 removed outlier: 3.963A pdb=" N PHE D 68 " --> pdb=" O SER D 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 65 through 68' Processing helix chain 'D' and resid 113 through 124 Processing helix chain 'D' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL D 176 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY D 215 " --> pdb=" O GLY D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG D 280 " --> pdb=" O LYS D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 289 removed outlier: 3.689A pdb=" N ASP D 289 " --> pdb=" O ILE D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 347 through 360 Processing helix chain 'E' and resid 4 through 9 Processing helix chain 'E' and resid 10 through 19 removed outlier: 3.760A pdb=" N LYS E 14 " --> pdb=" O ASN E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 57 Processing helix chain 'E' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE E 68 " --> pdb=" O SER E 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 65 through 68' Processing helix chain 'E' and resid 113 through 124 Processing helix chain 'E' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL E 176 " --> pdb=" O GLY E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY E 215 " --> pdb=" O GLY E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 Processing helix chain 'E' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS E 279 " --> pdb=" O GLU E 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG E 280 " --> pdb=" O LYS E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP E 289 " --> pdb=" O ILE E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 333 Processing helix chain 'E' and resid 347 through 360 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS F 14 " --> pdb=" O ASN F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 57 Processing helix chain 'F' and resid 65 through 68 removed outlier: 3.965A pdb=" N PHE F 68 " --> pdb=" O SER F 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 65 through 68' Processing helix chain 'F' and resid 113 through 124 Processing helix chain 'F' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL F 176 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY F 215 " --> pdb=" O GLY F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 263 Processing helix chain 'F' and resid 266 through 280 removed outlier: 3.740A pdb=" N LYS F 279 " --> pdb=" O GLU F 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG F 280 " --> pdb=" O LYS F 276 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP F 289 " --> pdb=" O ILE F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 333 Processing helix chain 'F' and resid 347 through 360 Processing helix chain 'G' and resid 4 through 9 Processing helix chain 'G' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS G 14 " --> pdb=" O ASN G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE G 68 " --> pdb=" O SER G 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 65 through 68' Processing helix chain 'G' and resid 113 through 124 Processing helix chain 'G' and resid 172 through 187 removed outlier: 3.665A pdb=" N VAL G 176 " --> pdb=" O GLY G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY G 215 " --> pdb=" O GLY G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 263 Processing helix chain 'G' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS G 279 " --> pdb=" O GLU G 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG G 280 " --> pdb=" O LYS G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP G 289 " --> pdb=" O ILE G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 333 Processing helix chain 'G' and resid 347 through 360 Processing helix chain 'H' and resid 4 through 9 Processing helix chain 'H' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS H 14 " --> pdb=" O ASN H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE H 68 " --> pdb=" O SER H 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 65 through 68' Processing helix chain 'H' and resid 113 through 124 Processing helix chain 'H' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL H 176 " --> pdb=" O GLY H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 233 removed outlier: 4.221A pdb=" N GLY H 215 " --> pdb=" O GLY H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 263 Processing helix chain 'H' and resid 266 through 280 removed outlier: 3.740A pdb=" N LYS H 279 " --> pdb=" O GLU H 275 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG H 280 " --> pdb=" O LYS H 276 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 289 removed outlier: 3.689A pdb=" N ASP H 289 " --> pdb=" O ILE H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 326 through 333 Processing helix chain 'H' and resid 347 through 360 Processing helix chain 'I' and resid 4 through 9 Processing helix chain 'I' and resid 10 through 19 removed outlier: 3.760A pdb=" N LYS I 14 " --> pdb=" O ASN I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE I 68 " --> pdb=" O SER I 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 65 through 68' Processing helix chain 'I' and resid 113 through 124 Processing helix chain 'I' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL I 176 " --> pdb=" O GLY I 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 233 removed outlier: 4.222A pdb=" N GLY I 215 " --> pdb=" O GLY I 211 " (cutoff:3.500A) Processing helix chain 'I' and resid 258 through 263 Processing helix chain 'I' and resid 266 through 280 removed outlier: 3.740A pdb=" N LYS I 279 " --> pdb=" O GLU I 275 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG I 280 " --> pdb=" O LYS I 276 " (cutoff:3.500A) Processing helix chain 'I' and resid 280 through 289 removed outlier: 3.691A pdb=" N ASP I 289 " --> pdb=" O ILE I 285 " (cutoff:3.500A) Processing helix chain 'I' and resid 326 through 333 Processing helix chain 'I' and resid 347 through 360 Processing helix chain 'J' and resid 4 through 9 Processing helix chain 'J' and resid 10 through 19 removed outlier: 3.759A pdb=" N LYS J 14 " --> pdb=" O ASN J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 53 through 57 Processing helix chain 'J' and resid 65 through 68 removed outlier: 3.964A pdb=" N PHE J 68 " --> pdb=" O SER J 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 65 through 68' Processing helix chain 'J' and resid 113 through 124 Processing helix chain 'J' and resid 172 through 187 removed outlier: 3.666A pdb=" N VAL J 176 " --> pdb=" O GLY J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 233 removed outlier: 4.222A pdb=" N GLY J 215 " --> pdb=" O GLY J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 258 through 263 Processing helix chain 'J' and resid 266 through 280 removed outlier: 3.739A pdb=" N LYS J 279 " --> pdb=" O GLU J 275 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG J 280 " --> pdb=" O LYS J 276 " (cutoff:3.500A) Processing helix chain 'J' and resid 280 through 289 removed outlier: 3.690A pdb=" N ASP J 289 " --> pdb=" O ILE J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 326 through 333 Processing helix chain 'J' and resid 347 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE A 98 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 96 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE A 33 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 101 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N CYS A 42 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA B 195 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 191 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE B 190 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY B 207 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 192 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 131 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE A 98 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET A 84 " --> pdb=" O LEU A 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU A 96 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE A 33 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A 101 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N CYS A 42 " --> pdb=" O ALA B 195 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA B 195 " --> pdb=" O CYS A 42 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY B 191 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE B 190 " --> pdb=" O GLY B 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY B 207 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY B 192 " --> pdb=" O GLN B 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE B 131 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 235 through 237 Processing sheet with id=AA4, first strand: chain 'A' and resid 235 through 237 removed outlier: 6.240A pdb=" N PHE A 131 " --> pdb=" O PRO A 208 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY A 192 " --> pdb=" O GLN A 205 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY A 207 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE A 190 " --> pdb=" O GLY A 207 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N GLY A 191 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA A 195 " --> pdb=" O CYS E 42 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N CYS E 42 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE E 33 " --> pdb=" O CYS E 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL E 101 " --> pdb=" O ILE E 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU E 96 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET E 84 " --> pdb=" O LEU E 96 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE E 98 " --> pdb=" O ALA E 82 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.739A pdb=" N PHE B 98 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 96 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE B 33 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 101 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N CYS B 42 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA C 195 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY C 191 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE C 190 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY C 207 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY C 192 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE C 131 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 63 removed outlier: 6.739A pdb=" N PHE B 98 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET B 84 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 96 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE B 33 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL B 101 " --> pdb=" O ILE B 33 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N CYS B 42 " --> pdb=" O ALA C 195 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N ALA C 195 " --> pdb=" O CYS B 42 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLY C 191 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE C 190 " --> pdb=" O GLY C 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY C 207 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY C 192 " --> pdb=" O GLN C 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE C 131 " --> pdb=" O PRO C 208 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE C 98 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 96 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE C 33 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 101 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS C 42 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA D 195 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY D 191 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE D 190 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY D 207 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 192 " --> pdb=" O GLN D 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE D 131 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE C 98 " --> pdb=" O ALA C 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET C 84 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU C 96 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE C 33 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 101 " --> pdb=" O ILE C 33 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS C 42 " --> pdb=" O ALA D 195 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ALA D 195 " --> pdb=" O CYS C 42 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY D 191 " --> pdb=" O THR C 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE D 190 " --> pdb=" O GLY D 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY D 207 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 192 " --> pdb=" O GLN D 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE D 131 " --> pdb=" O PRO D 208 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.737A pdb=" N PHE D 98 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET D 84 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU D 96 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE D 33 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL D 101 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N CYS D 42 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA E 195 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY E 191 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE E 190 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY E 207 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY E 192 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE E 131 " --> pdb=" O PRO E 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63 removed outlier: 6.737A pdb=" N PHE D 98 " --> pdb=" O ALA D 82 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET D 84 " --> pdb=" O LEU D 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU D 96 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE D 33 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL D 101 " --> pdb=" O ILE D 33 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N CYS D 42 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA E 195 " --> pdb=" O CYS D 42 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLY E 191 " --> pdb=" O THR D 46 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE E 190 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY E 207 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY E 192 " --> pdb=" O GLN E 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE E 131 " --> pdb=" O PRO E 208 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE F 98 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET F 84 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU F 96 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE F 33 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL F 101 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N CYS F 42 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA G 195 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY G 191 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE G 190 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY G 207 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY G 192 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE G 131 " --> pdb=" O PRO G 208 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE F 98 " --> pdb=" O ALA F 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET F 84 " --> pdb=" O LEU F 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU F 96 " --> pdb=" O MET F 84 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE F 33 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL F 101 " --> pdb=" O ILE F 33 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N CYS F 42 " --> pdb=" O ALA G 195 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N ALA G 195 " --> pdb=" O CYS F 42 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY G 191 " --> pdb=" O THR F 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE G 190 " --> pdb=" O GLY G 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY G 207 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY G 192 " --> pdb=" O GLN G 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE G 131 " --> pdb=" O PRO G 208 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 235 through 237 Processing sheet with id=AB5, first strand: chain 'F' and resid 235 through 237 removed outlier: 6.240A pdb=" N PHE F 131 " --> pdb=" O PRO F 208 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY F 192 " --> pdb=" O GLN F 205 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY F 207 " --> pdb=" O ILE F 190 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE F 190 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLY F 191 " --> pdb=" O THR J 46 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ALA F 195 " --> pdb=" O CYS J 42 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N CYS J 42 " --> pdb=" O ALA F 195 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE J 33 " --> pdb=" O CYS J 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL J 101 " --> pdb=" O ILE J 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU J 96 " --> pdb=" O MET J 84 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET J 84 " --> pdb=" O LEU J 96 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE J 98 " --> pdb=" O ALA J 82 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 60 through 63 removed outlier: 6.737A pdb=" N PHE G 98 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET G 84 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU G 96 " --> pdb=" O MET G 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE G 33 " --> pdb=" O CYS G 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL G 101 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N CYS G 42 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA H 195 " --> pdb=" O CYS G 42 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY H 191 " --> pdb=" O THR G 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE H 190 " --> pdb=" O GLY H 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY H 207 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY H 192 " --> pdb=" O GLN H 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE H 131 " --> pdb=" O PRO H 208 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 60 through 63 removed outlier: 6.737A pdb=" N PHE G 98 " --> pdb=" O ALA G 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET G 84 " --> pdb=" O LEU G 96 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU G 96 " --> pdb=" O MET G 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE G 33 " --> pdb=" O CYS G 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL G 101 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N CYS G 42 " --> pdb=" O ALA H 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA H 195 " --> pdb=" O CYS G 42 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLY H 191 " --> pdb=" O THR G 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE H 190 " --> pdb=" O GLY H 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY H 207 " --> pdb=" O ILE H 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY H 192 " --> pdb=" O GLN H 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE H 131 " --> pdb=" O PRO H 208 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE H 98 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET H 84 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU H 96 " --> pdb=" O MET H 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE H 33 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL H 101 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS H 42 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA I 195 " --> pdb=" O CYS H 42 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY I 191 " --> pdb=" O THR H 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE I 190 " --> pdb=" O GLY I 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY I 207 " --> pdb=" O ILE I 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY I 192 " --> pdb=" O GLN I 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE I 131 " --> pdb=" O PRO I 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE H 98 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET H 84 " --> pdb=" O LEU H 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU H 96 " --> pdb=" O MET H 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE H 33 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL H 101 " --> pdb=" O ILE H 33 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N CYS H 42 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N ALA I 195 " --> pdb=" O CYS H 42 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N GLY I 191 " --> pdb=" O THR H 46 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE I 190 " --> pdb=" O GLY I 207 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY I 207 " --> pdb=" O ILE I 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY I 192 " --> pdb=" O GLN I 205 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N PHE I 131 " --> pdb=" O PRO I 208 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE I 98 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET I 84 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU I 96 " --> pdb=" O MET I 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE I 33 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL I 101 " --> pdb=" O ILE I 33 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N CYS I 42 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA J 195 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY J 191 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE J 190 " --> pdb=" O GLY J 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY J 207 " --> pdb=" O ILE J 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY J 192 " --> pdb=" O GLN J 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE J 131 " --> pdb=" O PRO J 208 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 60 through 63 removed outlier: 6.738A pdb=" N PHE I 98 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N MET I 84 " --> pdb=" O LEU I 96 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU I 96 " --> pdb=" O MET I 84 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ILE I 33 " --> pdb=" O CYS I 99 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL I 101 " --> pdb=" O ILE I 33 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N CYS I 42 " --> pdb=" O ALA J 195 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ALA J 195 " --> pdb=" O CYS I 42 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY J 191 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE J 190 " --> pdb=" O GLY J 207 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N GLY J 207 " --> pdb=" O ILE J 190 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY J 192 " --> pdb=" O GLN J 205 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N PHE J 131 " --> pdb=" O PRO J 208 " (cutoff:3.500A) 1550 hydrogen bonds defined for protein. 4212 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: 10.33 Time building geometry restraints manager: 11.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 7322 1.33 - 1.45: 5427 1.45 - 1.57: 14951 1.57 - 1.69: 0 1.69 - 1.81: 330 Bond restraints: 28030 Sorted by residual: bond pdb=" C TRP G 149 " pdb=" N PRO G 150 " ideal model delta sigma weight residual 1.331 1.374 -0.044 1.31e-02 5.83e+03 1.12e+01 bond pdb=" C TRP A 149 " pdb=" N PRO A 150 " ideal model delta sigma weight residual 1.331 1.374 -0.044 1.31e-02 5.83e+03 1.11e+01 bond pdb=" C TRP H 149 " pdb=" N PRO H 150 " ideal model delta sigma weight residual 1.331 1.374 -0.044 1.31e-02 5.83e+03 1.11e+01 bond pdb=" C TRP E 149 " pdb=" N PRO E 150 " ideal model delta sigma weight residual 1.331 1.374 -0.043 1.31e-02 5.83e+03 1.10e+01 bond pdb=" C TRP J 149 " pdb=" N PRO J 150 " ideal model delta sigma weight residual 1.331 1.374 -0.043 1.31e-02 5.83e+03 1.10e+01 ... (remaining 28025 not shown) Histogram of bond angle deviations from ideal: 99.67 - 106.53: 1181 106.53 - 113.40: 13965 113.40 - 120.26: 10898 120.26 - 127.12: 11405 127.12 - 133.99: 441 Bond angle restraints: 37890 Sorted by residual: angle pdb=" N LYS G 95 " pdb=" CA LYS G 95 " pdb=" C LYS G 95 " ideal model delta sigma weight residual 109.40 119.59 -10.19 1.63e+00 3.76e-01 3.91e+01 angle pdb=" N LYS E 95 " pdb=" CA LYS E 95 " pdb=" C LYS E 95 " ideal model delta sigma weight residual 109.40 119.57 -10.17 1.63e+00 3.76e-01 3.89e+01 angle pdb=" N LYS J 95 " pdb=" CA LYS J 95 " pdb=" C LYS J 95 " ideal model delta sigma weight residual 109.40 119.57 -10.17 1.63e+00 3.76e-01 3.89e+01 angle pdb=" N LYS H 95 " pdb=" CA LYS H 95 " pdb=" C LYS H 95 " ideal model delta sigma weight residual 109.40 119.56 -10.16 1.63e+00 3.76e-01 3.89e+01 angle pdb=" N LYS B 95 " pdb=" CA LYS B 95 " pdb=" C LYS B 95 " ideal model delta sigma weight residual 109.40 119.55 -10.15 1.63e+00 3.76e-01 3.88e+01 ... (remaining 37885 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.43: 15172 15.43 - 30.85: 1095 30.85 - 46.28: 303 46.28 - 61.70: 70 61.70 - 77.13: 40 Dihedral angle restraints: 16680 sinusoidal: 6900 harmonic: 9780 Sorted by residual: dihedral pdb=" CA PRO G 160 " pdb=" C PRO G 160 " pdb=" N TYR G 161 " pdb=" CA TYR G 161 " ideal model delta harmonic sigma weight residual -180.00 -163.97 -16.03 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA PRO F 160 " pdb=" C PRO F 160 " pdb=" N TYR F 161 " pdb=" CA TYR F 161 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CA PRO A 160 " pdb=" C PRO A 160 " pdb=" N TYR A 161 " pdb=" CA TYR A 161 " ideal model delta harmonic sigma weight residual -180.00 -164.00 -16.00 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 16677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2743 0.053 - 0.105: 735 0.105 - 0.158: 185 0.158 - 0.210: 56 0.210 - 0.263: 61 Chirality restraints: 3780 Sorted by residual: chirality pdb=" CA LYS I 91 " pdb=" N LYS I 91 " pdb=" C LYS I 91 " pdb=" CB LYS I 91 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA LYS D 91 " pdb=" N LYS D 91 " pdb=" C LYS D 91 " pdb=" CB LYS D 91 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA LYS B 91 " pdb=" N LYS B 91 " pdb=" C LYS B 91 " pdb=" CB LYS B 91 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3777 not shown) Planarity restraints: 5030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY H 159 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO H 160 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO H 160 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO H 160 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 159 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO E 160 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO E 160 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 160 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY I 159 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO I 160 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO I 160 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO I 160 " 0.027 5.00e-02 4.00e+02 ... (remaining 5027 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6998 2.79 - 3.32: 24718 3.32 - 3.84: 48036 3.84 - 4.37: 58879 4.37 - 4.90: 97312 Nonbonded interactions: 235943 Sorted by model distance: nonbonded pdb=" OH TYR A 180 " pdb=" OG1 THR E 46 " model vdw 2.261 2.440 nonbonded pdb=" OG1 THR I 46 " pdb=" OH TYR J 180 " model vdw 2.262 2.440 nonbonded pdb=" OG1 THR D 46 " pdb=" OH TYR E 180 " model vdw 2.264 2.440 nonbonded pdb=" OH TYR F 180 " pdb=" OG1 THR J 46 " model vdw 2.265 2.440 nonbonded pdb=" OG1 THR H 46 " pdb=" OH TYR I 180 " model vdw 2.266 2.440 ... (remaining 235938 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 5.100 Check model and map are aligned: 0.390 Set scattering table: 0.260 Process input model: 69.820 Find NCS groups from input model: 1.660 Set up NCS constraints: 0.210 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: 0.000 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.006 0.044 28030 Z= 0.358 Angle : 0.920 10.193 37890 Z= 0.569 Chirality : 0.061 0.263 3780 Planarity : 0.005 0.048 5030 Dihedral : 12.590 77.128 10460 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.44 % Allowed : 7.07 % Favored : 90.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3390 helix: 1.36 (0.15), residues: 1090 sheet: -0.51 (0.17), residues: 840 loop : 0.43 (0.17), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 32 HIS 0.004 0.001 HIS E 284 PHE 0.020 0.002 PHE E 337 TYR 0.009 0.001 TYR C 137 ARG 0.006 0.001 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 685 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 615 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8041 (tttp) cc_final: 0.7803 (tttm) REVERT: A 120 ILE cc_start: 0.8728 (mm) cc_final: 0.8521 (mm) REVERT: A 173 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8583 (ttm-80) REVERT: A 334 LYS cc_start: 0.7261 (pttt) cc_final: 0.7054 (pttt) REVERT: B 76 ASP cc_start: 0.7908 (p0) cc_final: 0.7678 (p0) REVERT: B 77 MET cc_start: 0.9040 (mmm) cc_final: 0.8824 (mtp) REVERT: B 106 ARG cc_start: 0.8027 (mmt90) cc_final: 0.7670 (mpt180) REVERT: B 107 LYS cc_start: 0.8316 (mtpt) cc_final: 0.7687 (mmtm) REVERT: B 119 ARG cc_start: 0.8027 (mtp85) cc_final: 0.7778 (mtp85) REVERT: B 173 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8320 (ttm110) REVERT: B 210 GLU cc_start: 0.7732 (tp30) cc_final: 0.7153 (tp30) REVERT: B 336 TYR cc_start: 0.7762 (p90) cc_final: 0.7032 (p90) REVERT: B 363 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7473 (mt-10) REVERT: C 18 MET cc_start: 0.8984 (mmm) cc_final: 0.8775 (mmm) REVERT: C 84 MET cc_start: 0.8944 (ttp) cc_final: 0.8714 (ttp) REVERT: C 119 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7746 (mtp85) REVERT: C 263 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7173 (mt-10) REVERT: C 271 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7642 (mm-30) REVERT: C 334 LYS cc_start: 0.7415 (pttt) cc_final: 0.6852 (ptpp) REVERT: C 340 ARG cc_start: 0.7365 (ttm170) cc_final: 0.7155 (ttm110) REVERT: D 17 TYR cc_start: 0.9196 (m-80) cc_final: 0.8914 (m-80) REVERT: D 69 GLN cc_start: 0.8869 (pt0) cc_final: 0.8606 (pt0) REVERT: D 76 ASP cc_start: 0.8063 (p0) cc_final: 0.7850 (p0) REVERT: D 198 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8338 (mmp) REVERT: D 334 LYS cc_start: 0.7271 (pttt) cc_final: 0.6937 (ptpp) REVERT: E 24 ASP cc_start: 0.7944 (p0) cc_final: 0.7727 (p0) REVERT: E 69 GLN cc_start: 0.8935 (pt0) cc_final: 0.8708 (pt0) REVERT: E 119 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7768 (mtp85) REVERT: E 122 ASP cc_start: 0.8251 (m-30) cc_final: 0.8044 (m-30) REVERT: E 210 GLU cc_start: 0.7892 (tp30) cc_final: 0.7459 (tp30) REVERT: F 59 GLU cc_start: 0.8236 (mt-10) cc_final: 0.8012 (mt-10) REVERT: F 118 LYS cc_start: 0.8062 (tttp) cc_final: 0.7809 (tttm) REVERT: F 120 ILE cc_start: 0.8708 (mm) cc_final: 0.8505 (mm) REVERT: F 173 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8611 (ttm-80) REVERT: F 332 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7762 (tt0) REVERT: F 334 LYS cc_start: 0.7319 (pttt) cc_final: 0.6937 (pttt) REVERT: G 76 ASP cc_start: 0.7923 (p0) cc_final: 0.7694 (p0) REVERT: G 77 MET cc_start: 0.9047 (mmm) cc_final: 0.8834 (mtp) REVERT: G 106 ARG cc_start: 0.8003 (mmt90) cc_final: 0.7650 (mpt180) REVERT: G 107 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7730 (mmtm) REVERT: G 119 ARG cc_start: 0.8000 (mtp85) cc_final: 0.7748 (mtp85) REVERT: G 173 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8321 (ttm110) REVERT: G 210 GLU cc_start: 0.7728 (tp30) cc_final: 0.7149 (tp30) REVERT: G 334 LYS cc_start: 0.7226 (pttt) cc_final: 0.6910 (pttt) REVERT: G 336 TYR cc_start: 0.7772 (p90) cc_final: 0.7038 (p90) REVERT: H 18 MET cc_start: 0.8983 (mmm) cc_final: 0.8773 (mmm) REVERT: H 69 GLN cc_start: 0.8919 (pt0) cc_final: 0.8707 (pt0) REVERT: H 84 MET cc_start: 0.8956 (ttp) cc_final: 0.8721 (ttp) REVERT: H 119 ARG cc_start: 0.8009 (mtp85) cc_final: 0.7745 (mtp85) REVERT: H 263 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7286 (mt-10) REVERT: H 271 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7545 (mm-30) REVERT: H 334 LYS cc_start: 0.7409 (pttt) cc_final: 0.7016 (pttt) REVERT: H 340 ARG cc_start: 0.7369 (ttm170) cc_final: 0.7118 (ttm110) REVERT: H 363 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7222 (mt-10) REVERT: I 17 TYR cc_start: 0.9194 (m-80) cc_final: 0.8910 (m-80) REVERT: I 69 GLN cc_start: 0.8862 (pt0) cc_final: 0.8600 (pt0) REVERT: I 76 ASP cc_start: 0.8055 (p0) cc_final: 0.7838 (p0) REVERT: I 198 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8341 (mmp) REVERT: I 239 ASP cc_start: 0.8319 (t70) cc_final: 0.8088 (t70) REVERT: J 24 ASP cc_start: 0.7958 (p0) cc_final: 0.7727 (p0) REVERT: J 69 GLN cc_start: 0.8933 (pt0) cc_final: 0.8703 (pt0) REVERT: J 119 ARG cc_start: 0.8048 (mtp85) cc_final: 0.7749 (mtp85) REVERT: J 210 GLU cc_start: 0.7887 (tp30) cc_final: 0.7448 (tp30) REVERT: J 263 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7387 (mt-10) REVERT: J 334 LYS cc_start: 0.7134 (pttt) cc_final: 0.6911 (pttt) outliers start: 70 outliers final: 0 residues processed: 655 average time/residue: 1.4944 time to fit residues: 1124.3434 Evaluate side-chains 506 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 500 time to evaluate : 3.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain G residue 173 ARG Chi-restraints excluded: chain I residue 198 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 287 optimal weight: 6.9990 chunk 257 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 198 optimal weight: 10.0000 chunk 308 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 GLN A 194 ASN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 ASN ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 GLN C 69 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS ** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 152 ASN F 194 ASN ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 194 ASN ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 GLN ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 HIS I 194 ASN ** I 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 194 ASN ** J 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 28030 Z= 0.268 Angle : 0.570 5.920 37890 Z= 0.301 Chirality : 0.043 0.147 3780 Planarity : 0.005 0.043 5030 Dihedral : 4.946 59.628 3782 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.46 % Allowed : 12.13 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.15), residues: 3390 helix: 1.76 (0.15), residues: 1090 sheet: -0.10 (0.18), residues: 890 loop : 0.99 (0.19), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 32 HIS 0.004 0.001 HIS H 284 PHE 0.023 0.002 PHE G 89 TYR 0.010 0.001 TYR D 104 ARG 0.006 0.001 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 569 time to evaluate : 3.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7770 (mtp85) REVERT: A 227 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.7441 (mmm160) REVERT: A 332 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: B 105 ASN cc_start: 0.8621 (m-40) cc_final: 0.8415 (m110) REVERT: B 106 ARG cc_start: 0.8252 (mmt90) cc_final: 0.7953 (mmt-90) REVERT: B 107 LYS cc_start: 0.8446 (mtpt) cc_final: 0.7732 (mmtm) REVERT: B 119 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7739 (mtp85) REVERT: B 133 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8304 (mtp) REVERT: B 210 GLU cc_start: 0.7676 (tp30) cc_final: 0.7124 (tp30) REVERT: B 227 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.7695 (mmm160) REVERT: B 332 GLU cc_start: 0.7348 (tt0) cc_final: 0.6877 (tt0) REVERT: B 334 LYS cc_start: 0.7375 (ptmt) cc_final: 0.7088 (pttt) REVERT: B 363 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7411 (mt-10) REVERT: C 78 TYR cc_start: 0.7958 (m-80) cc_final: 0.7687 (m-10) REVERT: C 119 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7689 (mtp85) REVERT: C 203 GLU cc_start: 0.8412 (tt0) cc_final: 0.8159 (tt0) REVERT: C 227 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8001 (mmm160) REVERT: C 231 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8460 (m-30) REVERT: C 259 LYS cc_start: 0.7482 (tttt) cc_final: 0.7118 (ttmm) REVERT: C 263 GLU cc_start: 0.7557 (mt-10) cc_final: 0.7320 (mt-10) REVERT: D 69 GLN cc_start: 0.8828 (pt0) cc_final: 0.8569 (pt0) REVERT: D 77 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8383 (mmm) REVERT: D 332 GLU cc_start: 0.8178 (tp30) cc_final: 0.7740 (tt0) REVERT: D 334 LYS cc_start: 0.7408 (pttt) cc_final: 0.7179 (pttt) REVERT: D 337 PHE cc_start: 0.7844 (p90) cc_final: 0.7555 (p90) REVERT: E 24 ASP cc_start: 0.7949 (p0) cc_final: 0.7721 (p0) REVERT: E 78 TYR cc_start: 0.7976 (m-80) cc_final: 0.7744 (m-10) REVERT: E 115 HIS cc_start: 0.7658 (t-90) cc_final: 0.7456 (t-90) REVERT: E 119 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7748 (mtp85) REVERT: E 210 GLU cc_start: 0.7857 (tp30) cc_final: 0.7411 (tp30) REVERT: E 227 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.7489 (mmm160) REVERT: E 243 ILE cc_start: 0.7352 (OUTLIER) cc_final: 0.6977 (tp) REVERT: F 119 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7767 (mtp85) REVERT: F 210 GLU cc_start: 0.7787 (tp30) cc_final: 0.7509 (tp30) REVERT: F 227 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.7389 (mmm160) REVERT: F 259 LYS cc_start: 0.7346 (tttt) cc_final: 0.7087 (ttmm) REVERT: F 327 ARG cc_start: 0.6711 (tmt-80) cc_final: 0.6493 (tmt-80) REVERT: F 334 LYS cc_start: 0.7374 (pttt) cc_final: 0.7165 (pttt) REVERT: G 105 ASN cc_start: 0.8641 (m-40) cc_final: 0.8434 (m110) REVERT: G 106 ARG cc_start: 0.8228 (mmt90) cc_final: 0.7927 (mmt-90) REVERT: G 107 LYS cc_start: 0.8491 (mtpt) cc_final: 0.7774 (mmtm) REVERT: G 133 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8304 (mtp) REVERT: G 210 GLU cc_start: 0.7675 (tp30) cc_final: 0.7132 (tp30) REVERT: G 227 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.7751 (mmm160) REVERT: G 363 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7422 (mt-10) REVERT: H 59 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8103 (mt-10) REVERT: H 78 TYR cc_start: 0.7961 (m-80) cc_final: 0.7683 (m-10) REVERT: H 119 ARG cc_start: 0.7933 (mtp85) cc_final: 0.7687 (mtp85) REVERT: H 203 GLU cc_start: 0.8386 (tt0) cc_final: 0.8129 (tt0) REVERT: H 227 ARG cc_start: 0.9029 (OUTLIER) cc_final: 0.7987 (mmm160) REVERT: H 231 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8475 (m-30) REVERT: H 259 LYS cc_start: 0.7481 (tttt) cc_final: 0.7108 (ttmm) REVERT: H 263 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7319 (mt-10) REVERT: I 69 GLN cc_start: 0.8823 (pt0) cc_final: 0.8566 (pt0) REVERT: I 77 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8367 (mmm) REVERT: I 107 LYS cc_start: 0.8637 (mtpt) cc_final: 0.7917 (mmtm) REVERT: I 246 ASN cc_start: 0.4815 (OUTLIER) cc_final: 0.4589 (p0) REVERT: I 337 PHE cc_start: 0.7854 (p90) cc_final: 0.7565 (p90) REVERT: J 24 ASP cc_start: 0.7938 (p0) cc_final: 0.7712 (p0) REVERT: J 78 TYR cc_start: 0.8011 (m-80) cc_final: 0.7757 (m-10) REVERT: J 115 HIS cc_start: 0.7659 (t-90) cc_final: 0.7459 (t-90) REVERT: J 119 ARG cc_start: 0.8029 (mtp85) cc_final: 0.7705 (mtp85) REVERT: J 210 GLU cc_start: 0.7921 (tp30) cc_final: 0.7473 (tp30) REVERT: J 227 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.7479 (mmm160) REVERT: J 243 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.6974 (tp) REVERT: J 259 LYS cc_start: 0.7337 (tttt) cc_final: 0.6970 (tttp) REVERT: J 263 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7255 (mt-10) outliers start: 128 outliers final: 41 residues processed: 647 average time/residue: 1.5200 time to fit residues: 1128.5183 Evaluate side-chains 579 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 520 time to evaluate : 3.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 332 GLU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 77 MET Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 255 ASN Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain G residue 133 MET Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 255 ASN Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 257 SER Chi-restraints excluded: chain I residue 77 MET Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 246 ASN Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 165 VAL Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 171 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 256 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 309 optimal weight: 2.9990 chunk 334 optimal weight: 9.9990 chunk 275 optimal weight: 0.1980 chunk 306 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 69 GLN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS D 194 ASN D 253 HIS ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 ASN ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 28030 Z= 0.184 Angle : 0.527 6.208 37890 Z= 0.277 Chirality : 0.042 0.138 3780 Planarity : 0.004 0.046 5030 Dihedral : 4.114 19.925 3760 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.73 % Allowed : 15.09 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.47 (0.15), residues: 3390 helix: 2.01 (0.15), residues: 1090 sheet: -0.05 (0.17), residues: 890 loop : 1.08 (0.19), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 32 HIS 0.004 0.001 HIS D 253 PHE 0.024 0.002 PHE C 256 TYR 0.012 0.001 TYR A 104 ARG 0.009 0.000 ARG H 340 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 553 time to evaluate : 2.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8025 (mtp85) cc_final: 0.7757 (mtp85) REVERT: A 327 ARG cc_start: 0.6143 (mmt180) cc_final: 0.5802 (tmt-80) REVERT: B 84 MET cc_start: 0.8914 (ttp) cc_final: 0.8641 (ttp) REVERT: B 107 LYS cc_start: 0.8348 (mtpt) cc_final: 0.8093 (mtpp) REVERT: B 210 GLU cc_start: 0.7590 (tp30) cc_final: 0.7121 (tp30) REVERT: B 327 ARG cc_start: 0.6288 (mmt180) cc_final: 0.6014 (tmt-80) REVERT: B 332 GLU cc_start: 0.7291 (tt0) cc_final: 0.6784 (tt0) REVERT: B 334 LYS cc_start: 0.7559 (ptmt) cc_final: 0.7189 (pttt) REVERT: B 336 TYR cc_start: 0.8069 (p90) cc_final: 0.7421 (p90) REVERT: B 363 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7519 (mt-10) REVERT: C 59 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8078 (mt-10) REVERT: C 78 TYR cc_start: 0.7956 (m-80) cc_final: 0.7652 (m-10) REVERT: C 119 ARG cc_start: 0.7917 (mtp85) cc_final: 0.7705 (mtp85) REVERT: C 203 GLU cc_start: 0.8209 (tt0) cc_final: 0.7922 (tt0) REVERT: C 231 ASP cc_start: 0.8662 (OUTLIER) cc_final: 0.8405 (m-30) REVERT: C 246 ASN cc_start: 0.4733 (OUTLIER) cc_final: 0.4449 (p0) REVERT: C 259 LYS cc_start: 0.7502 (tttt) cc_final: 0.7123 (ttmm) REVERT: C 263 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7359 (mt-10) REVERT: C 327 ARG cc_start: 0.6086 (mmt180) cc_final: 0.5881 (tpt90) REVERT: C 332 GLU cc_start: 0.8122 (tp30) cc_final: 0.7882 (tt0) REVERT: D 69 GLN cc_start: 0.8839 (pt0) cc_final: 0.8612 (pt0) REVERT: D 77 MET cc_start: 0.8478 (mmm) cc_final: 0.8261 (mmm) REVERT: D 103 LYS cc_start: 0.8068 (OUTLIER) cc_final: 0.7774 (mttt) REVERT: D 107 LYS cc_start: 0.8590 (mtpt) cc_final: 0.7883 (mmtm) REVERT: D 214 MET cc_start: 0.8585 (tpt) cc_final: 0.8254 (tpp) REVERT: D 334 LYS cc_start: 0.7450 (pttt) cc_final: 0.7069 (ptpp) REVERT: D 337 PHE cc_start: 0.7636 (p90) cc_final: 0.7332 (p90) REVERT: E 24 ASP cc_start: 0.7952 (p0) cc_final: 0.7730 (p0) REVERT: E 119 ARG cc_start: 0.8024 (mtp85) cc_final: 0.7618 (mtp85) REVERT: E 210 GLU cc_start: 0.7838 (tp30) cc_final: 0.7316 (tp30) REVERT: E 243 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6944 (tp) REVERT: E 332 GLU cc_start: 0.7519 (tt0) cc_final: 0.7216 (tt0) REVERT: F 119 ARG cc_start: 0.8022 (mtp85) cc_final: 0.7756 (mtp85) REVERT: G 84 MET cc_start: 0.8952 (ttp) cc_final: 0.8675 (ttp) REVERT: G 107 LYS cc_start: 0.8429 (mtpt) cc_final: 0.8194 (mtpp) REVERT: G 119 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7947 (ttm-80) REVERT: G 210 GLU cc_start: 0.7557 (tp30) cc_final: 0.7070 (tp30) REVERT: G 327 ARG cc_start: 0.6319 (mmt180) cc_final: 0.6034 (tmt-80) REVERT: G 336 TYR cc_start: 0.8065 (p90) cc_final: 0.7414 (p90) REVERT: G 363 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7538 (mt-10) REVERT: H 59 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8078 (mt-10) REVERT: H 78 TYR cc_start: 0.7978 (m-80) cc_final: 0.7713 (m-10) REVERT: H 119 ARG cc_start: 0.7914 (mtp85) cc_final: 0.7706 (mtp85) REVERT: H 122 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: H 203 GLU cc_start: 0.8207 (tt0) cc_final: 0.7937 (tt0) REVERT: H 231 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: H 259 LYS cc_start: 0.7470 (tttt) cc_final: 0.7103 (ttmm) REVERT: H 263 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7369 (mt-10) REVERT: H 327 ARG cc_start: 0.6077 (mmt180) cc_final: 0.5876 (tpt90) REVERT: H 334 LYS cc_start: 0.7591 (pttt) cc_final: 0.7267 (ptpp) REVERT: I 69 GLN cc_start: 0.8837 (pt0) cc_final: 0.8612 (pt0) REVERT: I 77 MET cc_start: 0.8462 (mmm) cc_final: 0.8244 (mmm) REVERT: I 103 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7796 (mttt) REVERT: I 107 LYS cc_start: 0.8601 (mtpt) cc_final: 0.7893 (mmtm) REVERT: I 214 MET cc_start: 0.8593 (tpt) cc_final: 0.8178 (tpp) REVERT: I 337 PHE cc_start: 0.7625 (p90) cc_final: 0.7330 (p90) REVERT: J 24 ASP cc_start: 0.7936 (p0) cc_final: 0.7719 (p0) REVERT: J 119 ARG cc_start: 0.8036 (mtp85) cc_final: 0.7608 (mtp85) REVERT: J 210 GLU cc_start: 0.7833 (tp30) cc_final: 0.7279 (tp30) REVERT: J 243 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6942 (tp) REVERT: J 259 LYS cc_start: 0.7261 (tttt) cc_final: 0.6830 (tttp) REVERT: J 263 GLU cc_start: 0.7596 (mt-10) cc_final: 0.7253 (mt-10) REVERT: J 334 LYS cc_start: 0.6905 (pttt) cc_final: 0.6415 (ptpp) outliers start: 107 outliers final: 49 residues processed: 624 average time/residue: 1.4930 time to fit residues: 1070.4260 Evaluate side-chains 576 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 519 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 203 GLU Chi-restraints excluded: chain B residue 255 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain C residue 158 GLN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 246 ASN Chi-restraints excluded: chain F residue 255 ASN Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 203 GLU Chi-restraints excluded: chain G residue 246 ASN Chi-restraints excluded: chain G residue 255 ASN Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 158 GLN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 305 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 160 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 147 optimal weight: 7.9990 chunk 207 optimal weight: 1.9990 chunk 310 optimal weight: 7.9990 chunk 328 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 294 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 69 GLN C 74 ASN C 194 ASN ** C 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN G 362 ASN H 74 ASN ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 74 ASN ** I 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 28030 Z= 0.452 Angle : 0.622 6.947 37890 Z= 0.331 Chirality : 0.046 0.160 3780 Planarity : 0.005 0.051 5030 Dihedral : 4.669 24.263 3760 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.01 % Favored : 95.69 % Rotamer: Outliers : 5.37 % Allowed : 16.31 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 3390 helix: 1.69 (0.15), residues: 1090 sheet: -0.30 (0.17), residues: 910 loop : 0.98 (0.19), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 32 HIS 0.011 0.002 HIS D 253 PHE 0.022 0.002 PHE H 89 TYR 0.021 0.002 TYR J 78 ARG 0.009 0.001 ARG F 340 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 529 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7788 (mtp85) REVERT: A 134 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: A 210 GLU cc_start: 0.7819 (tp30) cc_final: 0.7548 (tp30) REVERT: A 227 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7536 (mmm160) REVERT: A 259 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6518 (ttmp) REVERT: A 332 GLU cc_start: 0.8077 (tp30) cc_final: 0.7589 (tt0) REVERT: A 334 LYS cc_start: 0.7346 (pttt) cc_final: 0.7072 (pttt) REVERT: B 107 LYS cc_start: 0.8300 (mtpt) cc_final: 0.7603 (mmtm) REVERT: B 119 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.7963 (ttm-80) REVERT: B 210 GLU cc_start: 0.7611 (tp30) cc_final: 0.7005 (tp30) REVERT: B 227 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7672 (mmm160) REVERT: B 327 ARG cc_start: 0.6249 (mmt180) cc_final: 0.6035 (tmt-80) REVERT: B 332 GLU cc_start: 0.7326 (tt0) cc_final: 0.6842 (tt0) REVERT: B 334 LYS cc_start: 0.7569 (ptmt) cc_final: 0.7263 (pttt) REVERT: C 78 TYR cc_start: 0.7915 (m-80) cc_final: 0.7690 (m-10) REVERT: C 119 ARG cc_start: 0.7989 (mtp85) cc_final: 0.7696 (mtp85) REVERT: C 227 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8010 (mmm160) REVERT: C 259 LYS cc_start: 0.7565 (tttt) cc_final: 0.7202 (ttmm) REVERT: C 263 GLU cc_start: 0.7523 (mt-10) cc_final: 0.7166 (mt-10) REVERT: D 69 GLN cc_start: 0.8909 (pt0) cc_final: 0.8675 (pt0) REVERT: D 103 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7631 (mttm) REVERT: D 106 ARG cc_start: 0.8666 (mpt180) cc_final: 0.8333 (mmt90) REVERT: D 107 LYS cc_start: 0.8523 (mtpt) cc_final: 0.7829 (mmtm) REVERT: D 198 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8423 (mmp) REVERT: D 334 LYS cc_start: 0.7448 (pttt) cc_final: 0.7069 (ptpp) REVERT: E 24 ASP cc_start: 0.7996 (p0) cc_final: 0.7782 (p0) REVERT: E 119 ARG cc_start: 0.8080 (mtp85) cc_final: 0.7701 (mtp85) REVERT: E 210 GLU cc_start: 0.7848 (tp30) cc_final: 0.7195 (tp30) REVERT: E 227 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.7564 (mmm160) REVERT: E 243 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.6945 (tp) REVERT: E 327 ARG cc_start: 0.6556 (mmt180) cc_final: 0.6181 (tpt170) REVERT: E 332 GLU cc_start: 0.7481 (tt0) cc_final: 0.7226 (tt0) REVERT: F 119 ARG cc_start: 0.8044 (mtp85) cc_final: 0.7783 (mtp85) REVERT: F 210 GLU cc_start: 0.7813 (tp30) cc_final: 0.7545 (tp30) REVERT: F 227 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7499 (mmm160) REVERT: F 332 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6830 (tt0) REVERT: G 107 LYS cc_start: 0.8363 (mtpt) cc_final: 0.7663 (mmtm) REVERT: G 210 GLU cc_start: 0.7607 (tp30) cc_final: 0.7006 (tp30) REVERT: G 227 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.7667 (mmm160) REVERT: G 327 ARG cc_start: 0.6257 (mmt180) cc_final: 0.6012 (tmt-80) REVERT: G 336 TYR cc_start: 0.8180 (p90) cc_final: 0.7442 (p90) REVERT: H 59 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8068 (mt-10) REVERT: H 119 ARG cc_start: 0.7967 (mtp85) cc_final: 0.7726 (mtp85) REVERT: H 122 ASP cc_start: 0.8178 (OUTLIER) cc_final: 0.7919 (m-30) REVERT: H 227 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.7972 (mmm160) REVERT: H 231 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8599 (m-30) REVERT: H 263 GLU cc_start: 0.7530 (mt-10) cc_final: 0.7190 (mt-10) REVERT: H 327 ARG cc_start: 0.6252 (mmt180) cc_final: 0.5850 (tpt90) REVERT: I 69 GLN cc_start: 0.8907 (pt0) cc_final: 0.8673 (pt0) REVERT: I 103 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7653 (mttm) REVERT: I 106 ARG cc_start: 0.8665 (mpt180) cc_final: 0.8330 (mmt90) REVERT: I 107 LYS cc_start: 0.8527 (mtpt) cc_final: 0.7817 (mmtm) REVERT: I 198 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8431 (mmp) REVERT: J 24 ASP cc_start: 0.7951 (p0) cc_final: 0.7744 (p0) REVERT: J 104 TYR cc_start: 0.7736 (OUTLIER) cc_final: 0.6581 (t80) REVERT: J 119 ARG cc_start: 0.8096 (mtp85) cc_final: 0.7694 (mtp85) REVERT: J 210 GLU cc_start: 0.7845 (tp30) cc_final: 0.7281 (tp30) REVERT: J 227 ARG cc_start: 0.9169 (OUTLIER) cc_final: 0.7555 (mmm160) REVERT: J 243 ILE cc_start: 0.7301 (OUTLIER) cc_final: 0.6914 (tp) REVERT: J 259 LYS cc_start: 0.7369 (tttt) cc_final: 0.6996 (tttp) REVERT: J 263 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7098 (mt-10) outliers start: 154 outliers final: 62 residues processed: 614 average time/residue: 1.5331 time to fit residues: 1078.5850 Evaluate side-chains 587 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 505 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 246 ASN Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 246 ASN Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 227 ARG Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 246 ASN Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 104 TYR Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 203 GLU Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 257 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 273 optimal weight: 0.7980 chunk 186 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 280 optimal weight: 0.0050 chunk 227 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 chunk 82 optimal weight: 0.2980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 8 HIS C 27 GLN C 253 HIS ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 126 ASN G 362 ASN H 8 HIS H 27 GLN H 74 ASN ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 28030 Z= 0.162 Angle : 0.524 7.879 37890 Z= 0.275 Chirality : 0.041 0.135 3780 Planarity : 0.004 0.044 5030 Dihedral : 4.069 21.109 3760 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.48 % Allowed : 18.78 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.47 (0.15), residues: 3390 helix: 2.05 (0.15), residues: 1090 sheet: -0.13 (0.17), residues: 910 loop : 1.12 (0.19), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 32 HIS 0.002 0.001 HIS C 253 PHE 0.022 0.001 PHE G 256 TYR 0.008 0.001 TYR E 104 ARG 0.009 0.000 ARG G 340 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 532 time to evaluate : 2.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7774 (mtp85) REVERT: A 332 GLU cc_start: 0.8120 (tp30) cc_final: 0.7709 (tt0) REVERT: B 15 GLN cc_start: 0.8202 (mm110) cc_final: 0.7934 (mm-40) REVERT: B 107 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7936 (mtpp) REVERT: B 210 GLU cc_start: 0.7517 (tp30) cc_final: 0.7037 (tp30) REVERT: B 227 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.7730 (mmm160) REVERT: B 332 GLU cc_start: 0.7348 (OUTLIER) cc_final: 0.6834 (tt0) REVERT: B 334 LYS cc_start: 0.7559 (ptmt) cc_final: 0.7237 (pttt) REVERT: B 336 TYR cc_start: 0.8038 (p90) cc_final: 0.7193 (p90) REVERT: C 59 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8022 (mt-10) REVERT: C 78 TYR cc_start: 0.7891 (m-80) cc_final: 0.7553 (m-10) REVERT: C 106 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.6918 (tpp80) REVERT: C 119 ARG cc_start: 0.7885 (mtp85) cc_final: 0.7601 (mtp85) REVERT: C 133 MET cc_start: 0.8401 (mtp) cc_final: 0.8092 (mtp) REVERT: C 214 MET cc_start: 0.8553 (tpt) cc_final: 0.8178 (tpp) REVERT: C 227 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7784 (mmm160) REVERT: C 246 ASN cc_start: 0.4670 (OUTLIER) cc_final: 0.4403 (p0) REVERT: C 259 LYS cc_start: 0.7584 (tttt) cc_final: 0.7220 (ttmm) REVERT: C 263 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7220 (mt-10) REVERT: C 327 ARG cc_start: 0.6293 (mmt180) cc_final: 0.5957 (tpt90) REVERT: C 334 LYS cc_start: 0.7583 (pttt) cc_final: 0.7238 (ptpp) REVERT: D 107 LYS cc_start: 0.8488 (mtpt) cc_final: 0.7784 (mmtm) REVERT: D 198 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8221 (mmp) REVERT: D 334 LYS cc_start: 0.7384 (pttt) cc_final: 0.7031 (ptpp) REVERT: E 119 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7615 (mtp85) REVERT: E 210 GLU cc_start: 0.7873 (tp30) cc_final: 0.7321 (tp30) REVERT: E 227 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.7557 (mmm160) REVERT: E 243 ILE cc_start: 0.7310 (OUTLIER) cc_final: 0.6947 (tp) REVERT: E 327 ARG cc_start: 0.6477 (mmt180) cc_final: 0.6240 (tpt170) REVERT: E 332 GLU cc_start: 0.7436 (tt0) cc_final: 0.7108 (tt0) REVERT: E 334 LYS cc_start: 0.7050 (pttt) cc_final: 0.6774 (pttp) REVERT: F 119 ARG cc_start: 0.8010 (mtp85) cc_final: 0.7793 (mtp85) REVERT: F 332 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: G 15 GLN cc_start: 0.8204 (mm110) cc_final: 0.7940 (mm-40) REVERT: G 227 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.7729 (mmm160) REVERT: G 332 GLU cc_start: 0.7758 (tp30) cc_final: 0.7166 (tm-30) REVERT: G 336 TYR cc_start: 0.8042 (p90) cc_final: 0.7121 (p90) REVERT: H 59 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8065 (mt-10) REVERT: H 105 ASN cc_start: 0.8606 (m110) cc_final: 0.8226 (p0) REVERT: H 133 MET cc_start: 0.8407 (mtp) cc_final: 0.8092 (mtp) REVERT: H 214 MET cc_start: 0.8544 (tpt) cc_final: 0.8169 (tpp) REVERT: H 231 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8366 (m-30) REVERT: H 259 LYS cc_start: 0.7455 (tttt) cc_final: 0.7105 (ttmm) REVERT: H 263 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7224 (mt-10) REVERT: H 327 ARG cc_start: 0.6280 (mmt180) cc_final: 0.5971 (tpt90) REVERT: I 103 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7896 (mtpt) REVERT: I 107 LYS cc_start: 0.8497 (mtpt) cc_final: 0.7781 (mmtm) REVERT: I 198 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8273 (mmp) REVERT: J 105 ASN cc_start: 0.8486 (OUTLIER) cc_final: 0.8264 (p0) REVERT: J 119 ARG cc_start: 0.8030 (mtp85) cc_final: 0.7627 (mtp85) REVERT: J 210 GLU cc_start: 0.7866 (tp30) cc_final: 0.7381 (tp30) REVERT: J 227 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.7549 (mmm160) REVERT: J 243 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6942 (tp) REVERT: J 259 LYS cc_start: 0.7313 (tttt) cc_final: 0.6991 (tttp) REVERT: J 263 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7189 (mt-10) REVERT: J 327 ARG cc_start: 0.6477 (mmt180) cc_final: 0.6211 (tpt170) outliers start: 100 outliers final: 41 residues processed: 588 average time/residue: 1.4998 time to fit residues: 1012.3715 Evaluate side-chains 570 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 513 time to evaluate : 2.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 267 LEU Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 246 ASN Chi-restraints excluded: chain F residue 255 ASN Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 246 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 105 ASN Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 203 GLU Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 246 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 110 optimal weight: 0.8980 chunk 295 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 328 optimal weight: 2.9990 chunk 273 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 69 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 74 ASN ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 28030 Z= 0.362 Angle : 0.595 7.399 37890 Z= 0.317 Chirality : 0.044 0.150 3780 Planarity : 0.005 0.046 5030 Dihedral : 4.518 24.142 3760 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.66 % Favored : 96.05 % Rotamer: Outliers : 4.29 % Allowed : 18.85 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.21 (0.15), residues: 3390 helix: 1.79 (0.15), residues: 1090 sheet: -0.31 (0.17), residues: 910 loop : 1.03 (0.19), residues: 1390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 32 HIS 0.010 0.001 HIS D 253 PHE 0.020 0.002 PHE I 204 TYR 0.014 0.001 TYR I 78 ARG 0.010 0.001 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 527 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ARG cc_start: 0.8063 (mtp85) cc_final: 0.7827 (mtp85) REVERT: A 134 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7494 (mt-10) REVERT: A 210 GLU cc_start: 0.7822 (tp30) cc_final: 0.7545 (tp30) REVERT: A 227 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7519 (mmm160) REVERT: A 332 GLU cc_start: 0.8127 (tp30) cc_final: 0.7515 (tt0) REVERT: B 105 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8155 (m110) REVERT: B 106 ARG cc_start: 0.8170 (mmt90) cc_final: 0.7855 (mmt90) REVERT: B 107 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7600 (mmtm) REVERT: B 210 GLU cc_start: 0.7602 (tp30) cc_final: 0.7044 (tp30) REVERT: B 227 ARG cc_start: 0.9071 (OUTLIER) cc_final: 0.7687 (mmm160) REVERT: B 332 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6888 (tt0) REVERT: B 334 LYS cc_start: 0.7561 (ptmt) cc_final: 0.7234 (pttt) REVERT: B 336 TYR cc_start: 0.8105 (p90) cc_final: 0.7254 (p90) REVERT: C 59 GLU cc_start: 0.8317 (mt-10) cc_final: 0.8083 (mt-10) REVERT: C 78 TYR cc_start: 0.7951 (m-80) cc_final: 0.7563 (m-10) REVERT: C 105 ASN cc_start: 0.8618 (OUTLIER) cc_final: 0.8266 (p0) REVERT: C 106 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7023 (tpp80) REVERT: C 119 ARG cc_start: 0.7955 (mtp85) cc_final: 0.7660 (mtp85) REVERT: C 227 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8023 (mmm160) REVERT: C 246 ASN cc_start: 0.4933 (OUTLIER) cc_final: 0.4629 (p0) REVERT: C 259 LYS cc_start: 0.7561 (tttt) cc_final: 0.7204 (ttmm) REVERT: C 263 GLU cc_start: 0.7562 (mt-10) cc_final: 0.7196 (mt-10) REVERT: C 327 ARG cc_start: 0.6322 (mmt180) cc_final: 0.5940 (tpt90) REVERT: C 334 LYS cc_start: 0.7559 (pttt) cc_final: 0.7208 (ptpp) REVERT: D 107 LYS cc_start: 0.8426 (mtpt) cc_final: 0.7770 (mmtm) REVERT: D 126 ASN cc_start: 0.8805 (OUTLIER) cc_final: 0.8352 (t0) REVERT: D 198 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8381 (mmp) REVERT: D 332 GLU cc_start: 0.8191 (tp30) cc_final: 0.7722 (tt0) REVERT: E 119 ARG cc_start: 0.7993 (mtp85) cc_final: 0.7639 (mtp85) REVERT: E 210 GLU cc_start: 0.7902 (tp30) cc_final: 0.7263 (tp30) REVERT: E 227 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.7542 (mmm160) REVERT: E 243 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6842 (tp) REVERT: E 327 ARG cc_start: 0.6422 (mmt180) cc_final: 0.6198 (tpt170) REVERT: E 332 GLU cc_start: 0.7459 (tt0) cc_final: 0.7165 (tt0) REVERT: F 119 ARG cc_start: 0.8038 (mtp85) cc_final: 0.7813 (mtp85) REVERT: F 227 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.7470 (mmm160) REVERT: F 332 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.6839 (tt0) REVERT: G 106 ARG cc_start: 0.8164 (mmt90) cc_final: 0.7462 (tpp-160) REVERT: G 107 LYS cc_start: 0.8375 (mtpt) cc_final: 0.7573 (mmtm) REVERT: G 210 GLU cc_start: 0.7586 (tp30) cc_final: 0.6971 (tp30) REVERT: G 227 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7683 (mmm160) REVERT: G 332 GLU cc_start: 0.7744 (tp30) cc_final: 0.7247 (tt0) REVERT: G 336 TYR cc_start: 0.8104 (p90) cc_final: 0.7223 (p90) REVERT: H 59 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8080 (mt-10) REVERT: H 105 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8305 (p0) REVERT: H 106 ARG cc_start: 0.8291 (tpp80) cc_final: 0.7969 (tpp-160) REVERT: H 122 ASP cc_start: 0.8203 (OUTLIER) cc_final: 0.7934 (m-30) REVERT: H 231 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8587 (m-30) REVERT: H 246 ASN cc_start: 0.4788 (OUTLIER) cc_final: 0.4529 (p0) REVERT: H 259 LYS cc_start: 0.7484 (tttt) cc_final: 0.7179 (ttmm) REVERT: H 263 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7316 (mt-10) REVERT: H 327 ARG cc_start: 0.6331 (mmt180) cc_final: 0.5954 (tpt90) REVERT: I 103 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7632 (mttm) REVERT: I 107 LYS cc_start: 0.8460 (mtpt) cc_final: 0.7786 (mmtm) REVERT: I 126 ASN cc_start: 0.8782 (OUTLIER) cc_final: 0.8319 (t0) REVERT: I 198 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8375 (mmp) REVERT: J 119 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7666 (mtp85) REVERT: J 210 GLU cc_start: 0.7873 (tp30) cc_final: 0.7292 (tp30) REVERT: J 227 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7532 (mmm160) REVERT: J 243 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6842 (tp) REVERT: J 259 LYS cc_start: 0.7391 (tttt) cc_final: 0.7084 (tttp) REVERT: J 263 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7179 (mt-10) outliers start: 123 outliers final: 53 residues processed: 596 average time/residue: 1.5291 time to fit residues: 1043.7063 Evaluate side-chains 594 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 516 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 227 ARG Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 257 SER Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 246 ASN Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 227 ARG Chi-restraints excluded: chain G residue 246 ASN Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 103 LYS Chi-restraints excluded: chain I residue 105 ASN Chi-restraints excluded: chain I residue 126 ASN Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 246 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 257 SER Chi-restraints excluded: chain J residue 267 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 317 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 187 optimal weight: 0.6980 chunk 240 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 276 optimal weight: 6.9990 chunk 183 optimal weight: 2.9990 chunk 327 optimal weight: 0.9990 chunk 205 optimal weight: 0.9980 chunk 199 optimal weight: 9.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 8 HIS ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 74 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 ASN G 8 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 GLN G 362 ASN H 74 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28030 Z= 0.227 Angle : 0.551 8.648 37890 Z= 0.290 Chirality : 0.042 0.137 3780 Planarity : 0.004 0.052 5030 Dihedral : 4.245 21.871 3760 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.04 % Favored : 96.67 % Rotamer: Outliers : 3.76 % Allowed : 19.79 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.46 (0.15), residues: 3390 helix: 1.96 (0.15), residues: 1080 sheet: -0.15 (0.17), residues: 890 loop : 1.19 (0.19), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 32 HIS 0.004 0.001 HIS C 253 PHE 0.023 0.002 PHE G 256 TYR 0.013 0.001 TYR I 78 ARG 0.012 0.001 ARG F 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 541 time to evaluate : 3.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.7563 (OUTLIER) cc_final: 0.6726 (t80) REVERT: A 105 ASN cc_start: 0.8492 (OUTLIER) cc_final: 0.8232 (p0) REVERT: A 119 ARG cc_start: 0.8088 (mtp85) cc_final: 0.7823 (mtp85) REVERT: A 227 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.7431 (mmm160) REVERT: A 327 ARG cc_start: 0.7281 (tmt-80) cc_final: 0.6781 (tpt90) REVERT: A 332 GLU cc_start: 0.8134 (tp30) cc_final: 0.7525 (tt0) REVERT: B 38 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8117 (pt0) REVERT: B 210 GLU cc_start: 0.7552 (tp30) cc_final: 0.6993 (tp30) REVERT: B 324 ARG cc_start: 0.7791 (ttp-170) cc_final: 0.7147 (ttp80) REVERT: B 332 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6886 (tt0) REVERT: B 336 TYR cc_start: 0.8106 (p90) cc_final: 0.7078 (p90) REVERT: C 59 GLU cc_start: 0.8304 (mt-10) cc_final: 0.8043 (mt-10) REVERT: C 78 TYR cc_start: 0.7975 (m-80) cc_final: 0.7623 (m-10) REVERT: C 105 ASN cc_start: 0.8624 (OUTLIER) cc_final: 0.8281 (p0) REVERT: C 106 ARG cc_start: 0.8195 (OUTLIER) cc_final: 0.6985 (tpp80) REVERT: C 133 MET cc_start: 0.8394 (mtp) cc_final: 0.8080 (mtp) REVERT: C 227 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8015 (mmm160) REVERT: C 246 ASN cc_start: 0.4715 (OUTLIER) cc_final: 0.4430 (p0) REVERT: C 259 LYS cc_start: 0.7560 (tttt) cc_final: 0.7219 (ttmm) REVERT: C 263 GLU cc_start: 0.7539 (mt-10) cc_final: 0.7177 (mt-10) REVERT: C 327 ARG cc_start: 0.6306 (mmt180) cc_final: 0.5998 (tpt90) REVERT: C 334 LYS cc_start: 0.7540 (pttt) cc_final: 0.7203 (ptpp) REVERT: D 107 LYS cc_start: 0.8396 (mtpt) cc_final: 0.7733 (mmtm) REVERT: D 198 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8291 (mmp) REVERT: D 332 GLU cc_start: 0.8170 (tp30) cc_final: 0.7702 (tt0) REVERT: E 119 ARG cc_start: 0.7943 (mtp85) cc_final: 0.7594 (mtp85) REVERT: E 210 GLU cc_start: 0.7921 (tp30) cc_final: 0.7329 (tp30) REVERT: E 227 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.7521 (mmm160) REVERT: E 243 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.6891 (tp) REVERT: E 327 ARG cc_start: 0.6381 (mmt180) cc_final: 0.6146 (tmt-80) REVERT: E 332 GLU cc_start: 0.7487 (tt0) cc_final: 0.7192 (tt0) REVERT: F 104 TYR cc_start: 0.7559 (OUTLIER) cc_final: 0.6576 (t80) REVERT: F 105 ASN cc_start: 0.8580 (OUTLIER) cc_final: 0.8247 (p0) REVERT: F 119 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7824 (mtp85) REVERT: F 134 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7403 (mt-10) REVERT: F 227 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7362 (mmm160) REVERT: F 327 ARG cc_start: 0.7009 (tmt-80) cc_final: 0.6786 (ptm-80) REVERT: F 332 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6889 (tt0) REVERT: G 38 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8152 (pt0) REVERT: G 105 ASN cc_start: 0.8565 (OUTLIER) cc_final: 0.7952 (p0) REVERT: G 106 ARG cc_start: 0.8062 (mmt90) cc_final: 0.7791 (mmt90) REVERT: G 107 LYS cc_start: 0.8364 (mtpt) cc_final: 0.7493 (mmtm) REVERT: G 210 GLU cc_start: 0.7532 (tp30) cc_final: 0.6988 (tp30) REVERT: G 327 ARG cc_start: 0.6992 (tmt-80) cc_final: 0.6682 (tmt-80) REVERT: G 332 GLU cc_start: 0.7777 (tp30) cc_final: 0.7011 (tm-30) REVERT: G 336 TYR cc_start: 0.8105 (p90) cc_final: 0.7068 (p90) REVERT: H 59 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8067 (mt-10) REVERT: H 105 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8339 (p0) REVERT: H 106 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7917 (tpp-160) REVERT: H 122 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: H 231 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8468 (m-30) REVERT: H 246 ASN cc_start: 0.4598 (OUTLIER) cc_final: 0.4355 (p0) REVERT: H 259 LYS cc_start: 0.7420 (tttt) cc_final: 0.7161 (ttmm) REVERT: H 263 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7360 (mt-10) REVERT: H 327 ARG cc_start: 0.6251 (mmt180) cc_final: 0.5958 (tpt90) REVERT: I 107 LYS cc_start: 0.8427 (mtpt) cc_final: 0.7754 (mmtm) REVERT: I 198 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8292 (mmp) REVERT: J 104 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.6588 (t80) REVERT: J 119 ARG cc_start: 0.8040 (mtp85) cc_final: 0.7620 (mtp85) REVERT: J 210 GLU cc_start: 0.7881 (tp30) cc_final: 0.7331 (tp30) REVERT: J 227 ARG cc_start: 0.9112 (OUTLIER) cc_final: 0.7517 (mmm160) REVERT: J 243 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.6886 (tp) REVERT: J 259 LYS cc_start: 0.7397 (tttt) cc_final: 0.6998 (tttp) REVERT: J 263 GLU cc_start: 0.7439 (mt-10) cc_final: 0.7099 (mt-10) REVERT: J 327 ARG cc_start: 0.6563 (mmt180) cc_final: 0.6161 (tmt-80) REVERT: J 358 THR cc_start: 0.8311 (m) cc_final: 0.8040 (t) outliers start: 108 outliers final: 50 residues processed: 601 average time/residue: 1.5755 time to fit residues: 1096.2325 Evaluate side-chains 596 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 519 time to evaluate : 2.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 104 TYR Chi-restraints excluded: chain F residue 105 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 246 ASN Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 246 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 75 SER Chi-restraints excluded: chain J residue 103 LYS Chi-restraints excluded: chain J residue 104 TYR Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 267 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 202 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 208 optimal weight: 2.9990 chunk 223 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 257 optimal weight: 0.0980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 74 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN F 152 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN H 74 ASN H 194 ASN H 205 GLN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 28030 Z= 0.278 Angle : 0.573 8.917 37890 Z= 0.302 Chirality : 0.043 0.142 3780 Planarity : 0.005 0.062 5030 Dihedral : 4.377 23.054 3760 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.54 % Favored : 96.17 % Rotamer: Outliers : 3.90 % Allowed : 20.35 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.37 (0.15), residues: 3390 helix: 1.91 (0.15), residues: 1080 sheet: -0.23 (0.17), residues: 890 loop : 1.13 (0.19), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 32 HIS 0.006 0.001 HIS D 253 PHE 0.017 0.002 PHE I 204 TYR 0.014 0.001 TYR I 78 ARG 0.012 0.001 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 529 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7974 (ttp) REVERT: A 104 TYR cc_start: 0.7538 (OUTLIER) cc_final: 0.6376 (t80) REVERT: A 105 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.8198 (p0) REVERT: A 134 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: A 227 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7471 (mmm160) REVERT: A 332 GLU cc_start: 0.8099 (tp30) cc_final: 0.7497 (tt0) REVERT: B 38 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8157 (pt0) REVERT: B 210 GLU cc_start: 0.7563 (tp30) cc_final: 0.6991 (tp30) REVERT: B 324 ARG cc_start: 0.7739 (ttp-170) cc_final: 0.7140 (ttp80) REVERT: B 332 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6890 (tt0) REVERT: B 336 TYR cc_start: 0.8117 (p90) cc_final: 0.7154 (p90) REVERT: C 59 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8056 (mt-10) REVERT: C 78 TYR cc_start: 0.8000 (m-80) cc_final: 0.7558 (m-10) REVERT: C 105 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8286 (p0) REVERT: C 106 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.6979 (tpp80) REVERT: C 133 MET cc_start: 0.8398 (mtp) cc_final: 0.8077 (mtp) REVERT: C 227 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8027 (mmm160) REVERT: C 246 ASN cc_start: 0.4875 (OUTLIER) cc_final: 0.4543 (p0) REVERT: C 259 LYS cc_start: 0.7577 (tttt) cc_final: 0.7229 (ttmm) REVERT: C 263 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7015 (mt-10) REVERT: C 334 LYS cc_start: 0.7519 (pttt) cc_final: 0.7200 (ptpp) REVERT: C 358 THR cc_start: 0.8426 (m) cc_final: 0.8097 (t) REVERT: D 107 LYS cc_start: 0.8388 (mtpt) cc_final: 0.7725 (mmtm) REVERT: D 198 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8343 (mmp) REVERT: D 334 LYS cc_start: 0.7327 (pttt) cc_final: 0.7103 (ptpp) REVERT: E 119 ARG cc_start: 0.7949 (mtp85) cc_final: 0.7595 (mtp85) REVERT: E 210 GLU cc_start: 0.7920 (tp30) cc_final: 0.7324 (tp30) REVERT: E 227 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.7506 (mmm160) REVERT: E 243 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6889 (tp) REVERT: E 332 GLU cc_start: 0.7471 (tt0) cc_final: 0.6977 (tt0) REVERT: E 334 LYS cc_start: 0.7194 (pttp) cc_final: 0.6568 (ptpp) REVERT: E 358 THR cc_start: 0.8327 (m) cc_final: 0.8056 (t) REVERT: F 29 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7954 (ttp) REVERT: F 134 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: F 158 GLN cc_start: 0.8679 (tt0) cc_final: 0.8455 (tt0) REVERT: F 227 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.7406 (mmm160) REVERT: F 327 ARG cc_start: 0.7133 (tmt-80) cc_final: 0.6755 (tpt90) REVERT: F 332 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6865 (tt0) REVERT: G 38 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8158 (pt0) REVERT: G 105 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.7867 (p0) REVERT: G 107 LYS cc_start: 0.8358 (mtpt) cc_final: 0.7503 (mmtm) REVERT: G 210 GLU cc_start: 0.7516 (tp30) cc_final: 0.6969 (tp30) REVERT: G 332 GLU cc_start: 0.7776 (tp30) cc_final: 0.7001 (tm-30) REVERT: G 336 TYR cc_start: 0.8123 (p90) cc_final: 0.7083 (p90) REVERT: H 59 GLU cc_start: 0.8276 (mt-10) cc_final: 0.8044 (mt-10) REVERT: H 105 ASN cc_start: 0.8607 (OUTLIER) cc_final: 0.8293 (p0) REVERT: H 106 ARG cc_start: 0.8300 (tpp80) cc_final: 0.7920 (tpp-160) REVERT: H 122 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7930 (m-30) REVERT: H 133 MET cc_start: 0.8397 (mtp) cc_final: 0.8088 (mtp) REVERT: H 231 ASP cc_start: 0.8680 (OUTLIER) cc_final: 0.8455 (m-30) REVERT: H 246 ASN cc_start: 0.4851 (OUTLIER) cc_final: 0.4590 (p0) REVERT: H 263 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7379 (mt-10) REVERT: H 327 ARG cc_start: 0.6250 (mmt180) cc_final: 0.5984 (tpt90) REVERT: I 107 LYS cc_start: 0.8398 (mtpt) cc_final: 0.7730 (mmtm) REVERT: I 198 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8358 (mmp) REVERT: J 119 ARG cc_start: 0.8051 (mtp85) cc_final: 0.7626 (mtp85) REVERT: J 210 GLU cc_start: 0.7861 (tp30) cc_final: 0.7292 (tp30) REVERT: J 227 ARG cc_start: 0.9133 (OUTLIER) cc_final: 0.7494 (mmm160) REVERT: J 243 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.6886 (tp) REVERT: J 263 GLU cc_start: 0.7445 (mt-10) cc_final: 0.6932 (pt0) REVERT: J 327 ARG cc_start: 0.6602 (mmt180) cc_final: 0.6155 (tmt-80) REVERT: J 358 THR cc_start: 0.8346 (m) cc_final: 0.8064 (t) outliers start: 112 outliers final: 58 residues processed: 591 average time/residue: 1.5139 time to fit residues: 1027.6583 Evaluate side-chains 605 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 520 time to evaluate : 3.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 103 LYS Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 123 MET Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 255 ASN Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 246 ASN Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 122 ASP Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain I residue 38 GLU Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 246 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 105 ASN Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 203 GLU Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 267 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 298 optimal weight: 6.9990 chunk 313 optimal weight: 7.9990 chunk 286 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 133 optimal weight: 3.9990 chunk 239 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 275 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 304 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 74 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN F 152 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 GLN G 362 ASN H 74 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28030 Z= 0.211 Angle : 0.554 10.198 37890 Z= 0.291 Chirality : 0.042 0.135 3780 Planarity : 0.004 0.052 5030 Dihedral : 4.196 21.541 3760 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.33 % Favored : 96.46 % Rotamer: Outliers : 3.66 % Allowed : 21.18 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.47 (0.15), residues: 3390 helix: 2.03 (0.15), residues: 1080 sheet: -0.19 (0.17), residues: 890 loop : 1.18 (0.19), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 32 HIS 0.004 0.001 HIS C 253 PHE 0.025 0.001 PHE B 256 TYR 0.015 0.001 TYR I 78 ARG 0.013 0.001 ARG J 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 530 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7940 (ttp) REVERT: A 105 ASN cc_start: 0.8304 (OUTLIER) cc_final: 0.8096 (p0) REVERT: A 119 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7876 (mtp85) REVERT: A 134 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7427 (mt-10) REVERT: A 227 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.7399 (mmm160) REVERT: A 332 GLU cc_start: 0.8110 (tp30) cc_final: 0.7492 (tt0) REVERT: B 105 ASN cc_start: 0.8440 (OUTLIER) cc_final: 0.7851 (p0) REVERT: B 106 ARG cc_start: 0.8048 (mmt90) cc_final: 0.7348 (mpt180) REVERT: B 107 LYS cc_start: 0.8338 (mtpt) cc_final: 0.7455 (mmtm) REVERT: B 324 ARG cc_start: 0.7756 (ttp-170) cc_final: 0.7171 (ttp80) REVERT: B 327 ARG cc_start: 0.6967 (ttt-90) cc_final: 0.6552 (mmt180) REVERT: B 332 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6928 (tt0) REVERT: B 336 TYR cc_start: 0.8119 (p90) cc_final: 0.7078 (p90) REVERT: C 59 GLU cc_start: 0.8324 (mt-10) cc_final: 0.8066 (mt-10) REVERT: C 78 TYR cc_start: 0.7988 (m-80) cc_final: 0.7630 (m-10) REVERT: C 105 ASN cc_start: 0.8623 (OUTLIER) cc_final: 0.8339 (p0) REVERT: C 106 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6975 (tpp80) REVERT: C 133 MET cc_start: 0.8379 (mtp) cc_final: 0.8073 (mtp) REVERT: C 227 ARG cc_start: 0.8951 (OUTLIER) cc_final: 0.7828 (mmm160) REVERT: C 246 ASN cc_start: 0.4832 (OUTLIER) cc_final: 0.4510 (p0) REVERT: C 259 LYS cc_start: 0.7619 (tttt) cc_final: 0.7333 (ttmm) REVERT: C 263 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7023 (mt-10) REVERT: C 334 LYS cc_start: 0.7489 (pttt) cc_final: 0.7186 (ptpp) REVERT: C 358 THR cc_start: 0.8554 (m) cc_final: 0.8250 (t) REVERT: D 106 ARG cc_start: 0.8458 (mpt180) cc_final: 0.8202 (mmt180) REVERT: D 107 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7731 (mmtm) REVERT: D 198 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8277 (mmp) REVERT: D 255 ASN cc_start: 0.7776 (m-40) cc_final: 0.7499 (m-40) REVERT: D 334 LYS cc_start: 0.7350 (pttt) cc_final: 0.7091 (ptpp) REVERT: E 119 ARG cc_start: 0.7932 (mtp85) cc_final: 0.7587 (mtp85) REVERT: E 210 GLU cc_start: 0.7964 (tp30) cc_final: 0.7414 (tp30) REVERT: E 227 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.7529 (mmm160) REVERT: E 243 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6889 (tp) REVERT: E 327 ARG cc_start: 0.6612 (mmt180) cc_final: 0.6220 (tmt-80) REVERT: E 332 GLU cc_start: 0.7499 (tt0) cc_final: 0.7201 (tt0) REVERT: E 334 LYS cc_start: 0.7248 (pttp) cc_final: 0.7030 (pttt) REVERT: E 358 THR cc_start: 0.8352 (m) cc_final: 0.8064 (t) REVERT: F 104 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.6891 (t80) REVERT: F 134 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: F 227 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7357 (mmm160) REVERT: F 327 ARG cc_start: 0.7147 (tmt-80) cc_final: 0.6613 (tpt90) REVERT: F 332 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6874 (tt0) REVERT: G 38 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8093 (pt0) REVERT: G 105 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.7837 (p0) REVERT: G 107 LYS cc_start: 0.8383 (mtpt) cc_final: 0.7565 (mmtm) REVERT: G 246 ASN cc_start: 0.3840 (OUTLIER) cc_final: 0.3521 (p0) REVERT: G 324 ARG cc_start: 0.7738 (ttp-170) cc_final: 0.7091 (ttp80) REVERT: G 336 TYR cc_start: 0.8118 (p90) cc_final: 0.6989 (p90) REVERT: H 59 GLU cc_start: 0.8274 (mt-10) cc_final: 0.8003 (mt-10) REVERT: H 105 ASN cc_start: 0.8538 (OUTLIER) cc_final: 0.8246 (p0) REVERT: H 106 ARG cc_start: 0.8258 (tpp80) cc_final: 0.7859 (tpp-160) REVERT: H 133 MET cc_start: 0.8400 (mtp) cc_final: 0.8091 (mtp) REVERT: H 231 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8485 (m-30) REVERT: H 246 ASN cc_start: 0.4739 (OUTLIER) cc_final: 0.4465 (p0) REVERT: H 263 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7341 (mt-10) REVERT: H 334 LYS cc_start: 0.7450 (pttt) cc_final: 0.7213 (pttp) REVERT: I 106 ARG cc_start: 0.8397 (mpt180) cc_final: 0.8120 (mmt180) REVERT: I 107 LYS cc_start: 0.8390 (mtpt) cc_final: 0.7706 (mmtm) REVERT: I 198 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8279 (mmp) REVERT: J 104 TYR cc_start: 0.7679 (OUTLIER) cc_final: 0.6492 (t80) REVERT: J 107 LYS cc_start: 0.8250 (mtpt) cc_final: 0.7623 (mmtm) REVERT: J 119 ARG cc_start: 0.8035 (mtp85) cc_final: 0.7618 (mtp85) REVERT: J 210 GLU cc_start: 0.7899 (tp30) cc_final: 0.7350 (tp30) REVERT: J 227 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.7522 (mmm160) REVERT: J 243 ILE cc_start: 0.7257 (OUTLIER) cc_final: 0.6884 (tp) REVERT: J 263 GLU cc_start: 0.7419 (mt-10) cc_final: 0.6931 (pt0) REVERT: J 327 ARG cc_start: 0.6514 (mmt180) cc_final: 0.6121 (tmt-80) REVERT: J 358 THR cc_start: 0.8321 (m) cc_final: 0.8047 (t) outliers start: 105 outliers final: 51 residues processed: 585 average time/residue: 1.4708 time to fit residues: 989.6836 Evaluate side-chains 586 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 508 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 246 ASN Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain C residue 267 LEU Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 75 SER Chi-restraints excluded: chain E residue 105 ASN Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 104 TYR Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 203 GLU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 255 ASN Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain F residue 332 GLU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 246 ASN Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain G residue 267 LEU Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 134 GLU Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 246 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 104 TYR Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 200 optimal weight: 8.9990 chunk 322 optimal weight: 3.9990 chunk 197 optimal weight: 9.9990 chunk 153 optimal weight: 4.9990 chunk 224 optimal weight: 5.9990 chunk 338 optimal weight: 7.9990 chunk 311 optimal weight: 0.9980 chunk 269 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 74 ASN C 205 GLN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 GLN F 152 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 362 ASN H 74 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 28030 Z= 0.410 Angle : 0.628 9.933 37890 Z= 0.332 Chirality : 0.046 0.157 3780 Planarity : 0.005 0.089 5030 Dihedral : 4.641 24.877 3760 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.92 % Favored : 95.78 % Rotamer: Outliers : 3.31 % Allowed : 21.95 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.08 (0.15), residues: 3390 helix: 1.68 (0.15), residues: 1090 sheet: -0.33 (0.17), residues: 890 loop : 0.90 (0.19), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 32 HIS 0.010 0.001 HIS D 253 PHE 0.021 0.002 PHE I 204 TYR 0.022 0.002 TYR H 104 ARG 0.013 0.001 ARG J 340 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6780 Ramachandran restraints generated. 3390 Oldfield, 0 Emsley, 3390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 517 time to evaluate : 3.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.8030 (ttp) REVERT: A 104 TYR cc_start: 0.7414 (OUTLIER) cc_final: 0.6695 (t80) REVERT: A 107 LYS cc_start: 0.8318 (mtmt) cc_final: 0.7753 (mmtm) REVERT: A 119 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7924 (mtp85) REVERT: A 134 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7501 (mt-10) REVERT: A 227 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.7531 (mmm160) REVERT: A 255 ASN cc_start: 0.7905 (OUTLIER) cc_final: 0.7321 (m-40) REVERT: A 332 GLU cc_start: 0.8132 (tp30) cc_final: 0.7610 (tt0) REVERT: B 105 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.7929 (p0) REVERT: B 106 ARG cc_start: 0.8261 (mmt90) cc_final: 0.7440 (mpt180) REVERT: B 107 LYS cc_start: 0.8332 (mtpt) cc_final: 0.7444 (mmtm) REVERT: B 210 GLU cc_start: 0.7631 (tp30) cc_final: 0.7042 (tp30) REVERT: B 327 ARG cc_start: 0.6981 (ttt-90) cc_final: 0.6622 (mpt180) REVERT: B 332 GLU cc_start: 0.7298 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: B 334 LYS cc_start: 0.7495 (ptmt) cc_final: 0.7215 (pttt) REVERT: B 336 TYR cc_start: 0.8127 (p90) cc_final: 0.7156 (p90) REVERT: C 59 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8116 (mt-10) REVERT: C 105 ASN cc_start: 0.8643 (OUTLIER) cc_final: 0.8302 (p0) REVERT: C 227 ARG cc_start: 0.9084 (OUTLIER) cc_final: 0.8018 (mmm160) REVERT: C 259 LYS cc_start: 0.7610 (tttt) cc_final: 0.7290 (ttmm) REVERT: C 263 GLU cc_start: 0.7322 (mt-10) cc_final: 0.6947 (mt-10) REVERT: C 334 LYS cc_start: 0.7593 (pttt) cc_final: 0.7239 (ptpp) REVERT: C 358 THR cc_start: 0.8379 (m) cc_final: 0.8080 (t) REVERT: D 106 ARG cc_start: 0.8520 (mpt180) cc_final: 0.8275 (mmt180) REVERT: D 107 LYS cc_start: 0.8397 (mtpt) cc_final: 0.7714 (mmtm) REVERT: D 198 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8443 (mmp) REVERT: D 332 GLU cc_start: 0.8214 (tp30) cc_final: 0.7689 (tt0) REVERT: E 210 GLU cc_start: 0.7918 (tp30) cc_final: 0.7276 (tp30) REVERT: E 227 ARG cc_start: 0.9161 (OUTLIER) cc_final: 0.7544 (mmm160) REVERT: E 243 ILE cc_start: 0.7272 (OUTLIER) cc_final: 0.6897 (tp) REVERT: E 332 GLU cc_start: 0.7472 (tt0) cc_final: 0.7091 (tt0) REVERT: E 334 LYS cc_start: 0.7260 (pttp) cc_final: 0.6624 (ptpp) REVERT: E 358 THR cc_start: 0.8265 (m) cc_final: 0.7974 (t) REVERT: F 29 MET cc_start: 0.8229 (OUTLIER) cc_final: 0.7987 (ttp) REVERT: F 134 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7421 (mt-10) REVERT: F 210 GLU cc_start: 0.7847 (tp30) cc_final: 0.7618 (tp30) REVERT: F 227 ARG cc_start: 0.9041 (OUTLIER) cc_final: 0.7474 (mmm160) REVERT: F 255 ASN cc_start: 0.7921 (OUTLIER) cc_final: 0.7322 (m-40) REVERT: F 327 ARG cc_start: 0.7218 (tmt-80) cc_final: 0.6582 (tpt90) REVERT: G 38 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8131 (pt0) REVERT: G 107 LYS cc_start: 0.8364 (mtpt) cc_final: 0.7591 (mmtm) REVERT: G 210 GLU cc_start: 0.7590 (tp30) cc_final: 0.7039 (tp30) REVERT: G 334 LYS cc_start: 0.7227 (pttt) cc_final: 0.6908 (pttp) REVERT: G 336 TYR cc_start: 0.8138 (p90) cc_final: 0.7170 (p90) REVERT: H 59 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8074 (mt-10) REVERT: H 104 TYR cc_start: 0.7466 (t80) cc_final: 0.7261 (t80) REVERT: H 105 ASN cc_start: 0.8553 (OUTLIER) cc_final: 0.8135 (p0) REVERT: H 106 ARG cc_start: 0.8212 (tpp80) cc_final: 0.7835 (tpp-160) REVERT: H 246 ASN cc_start: 0.4767 (OUTLIER) cc_final: 0.4500 (p0) REVERT: H 263 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7296 (mt-10) REVERT: I 106 ARG cc_start: 0.8466 (mpt180) cc_final: 0.8198 (mmt180) REVERT: I 107 LYS cc_start: 0.8402 (mtpt) cc_final: 0.7716 (mmtm) REVERT: I 198 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8419 (mmp) REVERT: I 332 GLU cc_start: 0.8042 (tp30) cc_final: 0.7401 (tp30) REVERT: J 104 TYR cc_start: 0.7658 (OUTLIER) cc_final: 0.6480 (t80) REVERT: J 107 LYS cc_start: 0.8324 (mtpt) cc_final: 0.7709 (mmtm) REVERT: J 119 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7660 (mtp85) REVERT: J 210 GLU cc_start: 0.7909 (tp30) cc_final: 0.7327 (tp30) REVERT: J 227 ARG cc_start: 0.9162 (OUTLIER) cc_final: 0.7533 (mmm160) REVERT: J 243 ILE cc_start: 0.7273 (OUTLIER) cc_final: 0.6894 (tp) REVERT: J 263 GLU cc_start: 0.7387 (mt-10) cc_final: 0.7161 (mt-10) REVERT: J 327 ARG cc_start: 0.6650 (mmt180) cc_final: 0.6147 (tmt-80) REVERT: J 332 GLU cc_start: 0.7600 (tp30) cc_final: 0.7346 (tt0) REVERT: J 334 LYS cc_start: 0.7445 (pttt) cc_final: 0.6754 (pttm) REVERT: J 358 THR cc_start: 0.8374 (m) cc_final: 0.8097 (t) outliers start: 95 outliers final: 52 residues processed: 569 average time/residue: 1.4861 time to fit residues: 971.0853 Evaluate side-chains 586 residues out of total 2870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 511 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 MET Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 134 GLU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain A residue 255 ASN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 267 LEU Chi-restraints excluded: chain B residue 105 ASN Chi-restraints excluded: chain B residue 152 ASN Chi-restraints excluded: chain B residue 257 SER Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain C residue 105 ASN Chi-restraints excluded: chain C residue 134 GLU Chi-restraints excluded: chain C residue 151 SER Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 227 ARG Chi-restraints excluded: chain C residue 257 SER Chi-restraints excluded: chain D residue 152 ASN Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 198 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 151 SER Chi-restraints excluded: chain E residue 152 ASN Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 203 GLU Chi-restraints excluded: chain E residue 227 ARG Chi-restraints excluded: chain E residue 243 ILE Chi-restraints excluded: chain E residue 246 ASN Chi-restraints excluded: chain E residue 267 LEU Chi-restraints excluded: chain F residue 29 MET Chi-restraints excluded: chain F residue 57 LEU Chi-restraints excluded: chain F residue 126 ASN Chi-restraints excluded: chain F residue 134 GLU Chi-restraints excluded: chain F residue 152 ASN Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 227 ARG Chi-restraints excluded: chain F residue 255 ASN Chi-restraints excluded: chain F residue 257 SER Chi-restraints excluded: chain F residue 267 LEU Chi-restraints excluded: chain G residue 38 GLU Chi-restraints excluded: chain G residue 105 ASN Chi-restraints excluded: chain G residue 151 SER Chi-restraints excluded: chain G residue 152 ASN Chi-restraints excluded: chain G residue 246 ASN Chi-restraints excluded: chain G residue 257 SER Chi-restraints excluded: chain H residue 105 ASN Chi-restraints excluded: chain H residue 151 SER Chi-restraints excluded: chain H residue 152 ASN Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 246 ASN Chi-restraints excluded: chain I residue 151 SER Chi-restraints excluded: chain I residue 152 ASN Chi-restraints excluded: chain I residue 165 VAL Chi-restraints excluded: chain I residue 198 MET Chi-restraints excluded: chain I residue 212 ILE Chi-restraints excluded: chain I residue 246 ASN Chi-restraints excluded: chain I residue 267 LEU Chi-restraints excluded: chain J residue 3 THR Chi-restraints excluded: chain J residue 104 TYR Chi-restraints excluded: chain J residue 152 ASN Chi-restraints excluded: chain J residue 203 GLU Chi-restraints excluded: chain J residue 227 ARG Chi-restraints excluded: chain J residue 243 ILE Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 267 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 340 random chunks: chunk 214 optimal weight: 5.9990 chunk 287 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 248 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 270 optimal weight: 0.9990 chunk 113 optimal weight: 0.3980 chunk 277 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 362 ASN C 74 ASN ** D 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS F 152 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 GLN G 362 ASN H 74 ASN ** I 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.154260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.097641 restraints weight = 30876.836| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.19 r_work: 0.2861 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28030 Z= 0.186 Angle : 0.560 11.269 37890 Z= 0.294 Chirality : 0.042 0.137 3780 Planarity : 0.004 0.055 5030 Dihedral : 4.213 21.429 3760 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.19 % Favored : 96.64 % Rotamer: Outliers : 2.82 % Allowed : 22.68 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.15), residues: 3390 helix: 1.97 (0.15), residues: 1080 sheet: -0.21 (0.18), residues: 890 loop : 1.11 (0.19), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 32 HIS 0.003 0.001 HIS B 284 PHE 0.026 0.001 PHE G 256 TYR 0.018 0.001 TYR C 104 ARG 0.014 0.001 ARG J 340 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14144.70 seconds wall clock time: 250 minutes 8.47 seconds (15008.47 seconds total)