Starting phenix.real_space_refine on Mon Jul 22 05:44:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkb_36367/07_2024/8jkb_36367.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkb_36367/07_2024/8jkb_36367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkb_36367/07_2024/8jkb_36367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkb_36367/07_2024/8jkb_36367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkb_36367/07_2024/8jkb_36367.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkb_36367/07_2024/8jkb_36367.cif" } resolution = 3.27 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= -0.002 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 10647 2.51 5 N 3050 2.21 5 O 3332 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "E GLU 166": "OE1" <-> "OE2" Residue "E GLU 200": "OE1" <-> "OE2" Residue "E GLU 208": "OE1" <-> "OE2" Residue "I GLU 138": "OE1" <-> "OE2" Residue "I GLU 172": "OE1" <-> "OE2" Residue "I PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 290": "OD1" <-> "OD2" Residue "M GLU 17": "OE1" <-> "OE2" Residue "J GLU 138": "OE1" <-> "OE2" Residue "J PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N GLU 17": "OE1" <-> "OE2" Residue "K GLU 215": "OE1" <-> "OE2" Residue "K PHE 234": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 312": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 17169 Number of models: 1 Model: "" Number of chains: 15 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "F" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "L" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 404 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain breaks: 1 Chain: "H" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Chain: "C" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 400 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Chain breaks: 1 Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Link IDs: {'TRANS': 50} Chain breaks: 1 Chain: "E" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 410 Classifications: {'peptide': 51} Link IDs: {'TRANS': 50} Chain breaks: 1 Chain: "I" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "M" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "J" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "N" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "K" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "O" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Time building chain proxies: 9.51, per 1000 atoms: 0.55 Number of scatterers: 17169 At special positions: 0 Unit cell: (160.82, 165.98, 73.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 3332 8.00 N 3050 7.00 C 10647 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: 5.69 Conformation dependent library (CDL) restraints added in 2.9 seconds 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4154 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 41 sheets defined 16.4% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 removed outlier: 4.196A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA B 24 " --> pdb=" O ASP B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.567A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.948A pdb=" N LYS G 20 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.100A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.827A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'F' and resid 4 through 26 removed outlier: 3.869A pdb=" N ALA F 24 " --> pdb=" O ASP F 20 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N CYS F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA F 26 " --> pdb=" O ARG F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 35 Processing helix chain 'L' and resid 8 through 24 removed outlier: 3.749A pdb=" N MET L 21 " --> pdb=" O GLU L 17 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN L 24 " --> pdb=" O LYS L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 44 removed outlier: 3.828A pdb=" N HIS L 44 " --> pdb=" O TYR L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 48 removed outlier: 3.882A pdb=" N ASP L 48 " --> pdb=" O ALA L 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 45 through 48' Processing helix chain 'A' and resid 168 through 174 removed outlier: 3.645A pdb=" N THR A 174 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 174 removed outlier: 3.804A pdb=" N MET H 171 " --> pdb=" O GLU H 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 166 No H-bonds generated for 'chain 'C' and resid 164 through 166' Processing helix chain 'C' and resid 167 through 174 removed outlier: 3.740A pdb=" N MET C 171 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 174 " --> pdb=" O GLN C 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 removed outlier: 4.150A pdb=" N MET D 171 " --> pdb=" O GLU D 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 173 Processing helix chain 'I' and resid 4 through 25 removed outlier: 3.895A pdb=" N ALA I 24 " --> pdb=" O ASP I 20 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N CYS I 25 " --> pdb=" O ALA I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 35 removed outlier: 3.646A pdb=" N ILE I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) Processing helix chain 'M' and resid 8 through 24 removed outlier: 3.515A pdb=" N LYS M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET M 21 " --> pdb=" O GLU M 17 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASN M 24 " --> pdb=" O LYS M 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 44 Processing helix chain 'M' and resid 45 through 48 removed outlier: 3.932A pdb=" N ASP M 48 " --> pdb=" O ALA M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 45 through 48' Processing helix chain 'J' and resid 4 through 24 removed outlier: 3.903A pdb=" N ALA J 24 " --> pdb=" O ASP J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 35 removed outlier: 3.634A pdb=" N ILE J 33 " --> pdb=" O THR J 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 8 through 24 removed outlier: 3.983A pdb=" N GLU N 17 " --> pdb=" O ARG N 13 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN N 24 " --> pdb=" O LYS N 20 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 44 removed outlier: 4.089A pdb=" N ALA N 33 " --> pdb=" O LYS N 29 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS N 44 " --> pdb=" O TYR N 40 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 48 removed outlier: 3.880A pdb=" N ASP N 48 " --> pdb=" O ALA N 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 45 through 48' Processing helix chain 'K' and resid 4 through 25 removed outlier: 3.850A pdb=" N ALA K 24 " --> pdb=" O ASP K 20 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS K 25 " --> pdb=" O ALA K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 35 Processing helix chain 'O' and resid 8 through 24 removed outlier: 3.586A pdb=" N LYS O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET O 21 " --> pdb=" O GLU O 17 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN O 24 " --> pdb=" O LYS O 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 44 removed outlier: 3.797A pdb=" N ALA O 33 " --> pdb=" O LYS O 29 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU O 37 " --> pdb=" O ALA O 33 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS O 44 " --> pdb=" O TYR O 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.892A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.990A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 81 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.117A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 148 through 153 removed outlier: 3.929A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.507A pdb=" N SER B 191 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.823A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 242 " --> pdb=" O CYS B 233 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.438A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 49 through 51 removed outlier: 3.792A pdb=" N ARG F 49 " --> pdb=" O ILE F 338 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE F 338 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY F 330 " --> pdb=" O CYS F 317 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N CYS F 317 " --> pdb=" O GLY F 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 60 through 63 removed outlier: 3.953A pdb=" N ALA F 60 " --> pdb=" O ALA F 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 73 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU F 70 " --> pdb=" O TRP F 82 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE F 81 " --> pdb=" O HIS F 91 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N HIS F 91 " --> pdb=" O ILE F 81 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ASP F 83 " --> pdb=" O LYS F 89 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS F 89 " --> pdb=" O ASP F 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 104 through 105 removed outlier: 3.787A pdb=" N ALA F 104 " --> pdb=" O ALA F 113 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA F 113 " --> pdb=" O ALA F 104 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 112 " --> pdb=" O TYR F 124 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER F 122 " --> pdb=" O CYS F 114 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS F 121 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG F 137 " --> pdb=" O ILE F 123 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN F 125 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N VAL F 135 " --> pdb=" O ASN F 125 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 148 through 153 removed outlier: 6.356A pdb=" N CYS F 149 " --> pdb=" O SER F 160 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N SER F 160 " --> pdb=" O CYS F 149 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N PHE F 151 " --> pdb=" O VAL F 158 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL F 158 " --> pdb=" O PHE F 151 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP F 153 " --> pdb=" O GLN F 156 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE F 157 " --> pdb=" O TRP F 169 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA F 167 " --> pdb=" O THR F 159 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N CYS F 166 " --> pdb=" O PHE F 180 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N THR F 178 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ASP F 170 " --> pdb=" O GLN F 176 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLN F 176 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 190 through 192 removed outlier: 3.922A pdb=" N PHE F 199 " --> pdb=" O TRP F 211 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS F 209 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 229 through 232 removed outlier: 4.252A pdb=" N ALA F 231 " --> pdb=" O GLY F 244 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE F 241 " --> pdb=" O PHE F 253 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU F 252 " --> pdb=" O MET F 262 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N MET F 262 " --> pdb=" O LEU F 252 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP F 254 " --> pdb=" O GLU F 260 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLU F 260 " --> pdb=" O ASP F 254 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 273 through 278 removed outlier: 4.460A pdb=" N SER F 275 " --> pdb=" O GLY F 288 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 285 " --> pdb=" O TRP F 297 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA F 287 " --> pdb=" O ASN F 295 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN F 295 " --> pdb=" O ALA F 287 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY F 306 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 157 through 160 Processing sheet with id=AB7, first strand: chain 'A' and resid 163 through 164 removed outlier: 3.754A pdb=" N CYS A 163 " --> pdb=" O PHE A 201 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 157 through 164 removed outlier: 3.567A pdb=" N CYS H 163 " --> pdb=" O PHE H 201 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLU H 200 " --> pdb=" O ILE H 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 157 through 161 removed outlier: 3.579A pdb=" N VAL C 157 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 156 through 163 removed outlier: 3.876A pdb=" N CYS D 163 " --> pdb=" O PHE D 201 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 157 through 164 removed outlier: 3.686A pdb=" N CYS E 163 " --> pdb=" O PHE E 201 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 200 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLN E 183 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 46 through 51 removed outlier: 4.021A pdb=" N ARG I 46 " --> pdb=" O ASN I 340 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASN I 340 " --> pdb=" O ARG I 46 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE I 338 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR I 50 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU I 336 " --> pdb=" O THR I 50 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY I 330 " --> pdb=" O CYS I 317 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS I 317 " --> pdb=" O GLY I 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 60 through 63 removed outlier: 3.919A pdb=" N ALA I 60 " --> pdb=" O ALA I 73 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA I 73 " --> pdb=" O ALA I 60 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU I 70 " --> pdb=" O TRP I 82 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU I 79 " --> pdb=" O ALA I 92 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA I 92 " --> pdb=" O LEU I 79 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE I 81 " --> pdb=" O VAL I 90 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN I 88 " --> pdb=" O ASP I 83 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 104 through 105 removed outlier: 3.676A pdb=" N CYS I 121 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG I 137 " --> pdb=" O ILE I 123 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ASN I 125 " --> pdb=" O VAL I 135 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL I 135 " --> pdb=" O ASN I 125 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 148 through 153 removed outlier: 3.837A pdb=" N CYS I 148 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN I 156 " --> pdb=" O LEU I 152 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE I 157 " --> pdb=" O TRP I 169 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA I 167 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N CYS I 166 " --> pdb=" O PHE I 180 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR I 178 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N ASP I 170 " --> pdb=" O GLN I 176 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN I 176 " --> pdb=" O ASP I 170 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 190 through 192 removed outlier: 3.524A pdb=" N VAL I 200 " --> pdb=" O SER I 191 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE I 199 " --> pdb=" O TRP I 211 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU I 210 " --> pdb=" O GLN I 220 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN I 220 " --> pdb=" O LEU I 210 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 232 through 234 removed outlier: 3.582A pdb=" N PHE I 241 " --> pdb=" O PHE I 253 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N CYS I 250 " --> pdb=" O TYR I 264 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU I 252 " --> pdb=" O MET I 262 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N MET I 262 " --> pdb=" O LEU I 252 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ASP I 254 " --> pdb=" O GLU I 260 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU I 260 " --> pdb=" O ASP I 254 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 273 through 278 removed outlier: 4.557A pdb=" N SER I 275 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU I 285 " --> pdb=" O TRP I 297 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA I 287 " --> pdb=" O ASN I 295 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN I 295 " --> pdb=" O ALA I 287 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N CYS I 294 " --> pdb=" O LEU I 308 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 47 through 51 removed outlier: 4.119A pdb=" N ARG J 49 " --> pdb=" O ILE J 338 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA J 328 " --> pdb=" O LEU J 318 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU J 318 " --> pdb=" O ALA J 328 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY J 330 " --> pdb=" O SER J 316 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 60 through 63 removed outlier: 3.979A pdb=" N ALA J 60 " --> pdb=" O ALA J 73 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA J 73 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU J 70 " --> pdb=" O TRP J 82 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU J 79 " --> pdb=" O ALA J 92 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA J 92 " --> pdb=" O LEU J 79 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE J 81 " --> pdb=" O VAL J 90 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN J 88 " --> pdb=" O ASP J 83 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 100 through 105 removed outlier: 7.246A pdb=" N GLY J 115 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N CYS J 103 " --> pdb=" O ALA J 113 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA J 113 " --> pdb=" O CYS J 103 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL J 112 " --> pdb=" O TYR J 124 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS J 114 " --> pdb=" O SER J 122 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER J 122 " --> pdb=" O CYS J 114 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG J 137 " --> pdb=" O ILE J 123 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASN J 125 " --> pdb=" O VAL J 135 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL J 135 " --> pdb=" O ASN J 125 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 148 through 153 removed outlier: 3.673A pdb=" N CYS J 148 " --> pdb=" O SER J 160 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLN J 156 " --> pdb=" O LEU J 152 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ILE J 157 " --> pdb=" O TRP J 169 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA J 167 " --> pdb=" O THR J 159 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N CYS J 166 " --> pdb=" O PHE J 180 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR J 178 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP J 170 " --> pdb=" O GLN J 176 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN J 176 " --> pdb=" O ASP J 170 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 190 through 192 removed outlier: 3.808A pdb=" N PHE J 199 " --> pdb=" O TRP J 211 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS J 209 " --> pdb=" O SER J 201 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU J 210 " --> pdb=" O GLN J 220 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N GLN J 220 " --> pdb=" O LEU J 210 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 229 through 234 removed outlier: 4.249A pdb=" N ALA J 231 " --> pdb=" O GLY J 244 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR J 249 " --> pdb=" O SER J 245 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 273 through 278 removed outlier: 4.540A pdb=" N SER J 275 " --> pdb=" O GLY J 288 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU J 285 " --> pdb=" O TRP J 297 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA J 287 " --> pdb=" O ASN J 295 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ASN J 295 " --> pdb=" O ALA J 287 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY J 306 " --> pdb=" O VAL J 296 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 47 through 51 removed outlier: 3.985A pdb=" N ARG K 49 " --> pdb=" O ILE K 338 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY K 330 " --> pdb=" O CYS K 317 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS K 317 " --> pdb=" O GLY K 330 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 60 through 63 removed outlier: 3.802A pdb=" N ALA K 60 " --> pdb=" O ALA K 73 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA K 73 " --> pdb=" O ALA K 60 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE K 81 " --> pdb=" O HIS K 91 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS K 91 " --> pdb=" O ILE K 81 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ASP K 83 " --> pdb=" O LYS K 89 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LYS K 89 " --> pdb=" O ASP K 83 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 100 through 105 removed outlier: 7.287A pdb=" N GLY K 115 " --> pdb=" O MET K 101 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N CYS K 103 " --> pdb=" O ALA K 113 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA K 113 " --> pdb=" O CYS K 103 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL K 112 " --> pdb=" O TYR K 124 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER K 122 " --> pdb=" O CYS K 114 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE K 123 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASN K 125 " --> pdb=" O ARG K 134 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG K 134 " --> pdb=" O ASN K 125 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'K' and resid 148 through 153 removed outlier: 3.872A pdb=" N CYS K 148 " --> pdb=" O SER K 160 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE K 157 " --> pdb=" O TRP K 169 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA K 167 " --> pdb=" O THR K 159 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS K 166 " --> pdb=" O PHE K 180 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR K 178 " --> pdb=" O LEU K 168 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N ASP K 170 " --> pdb=" O GLN K 176 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN K 176 " --> pdb=" O ASP K 170 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 190 through 192 removed outlier: 3.556A pdb=" N SER K 191 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL K 200 " --> pdb=" O SER K 191 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE K 199 " --> pdb=" O TRP K 211 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS K 209 " --> pdb=" O SER K 201 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 229 through 234 removed outlier: 4.044A pdb=" N ALA K 231 " --> pdb=" O GLY K 244 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU K 252 " --> pdb=" O MET K 262 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET K 262 " --> pdb=" O LEU K 252 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 273 through 278 removed outlier: 4.555A pdb=" N SER K 275 " --> pdb=" O GLY K 288 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU K 285 " --> pdb=" O TRP K 297 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA K 287 " --> pdb=" O ASN K 295 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASN K 295 " --> pdb=" O ALA K 287 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS K 294 " --> pdb=" O LEU K 308 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY K 306 " --> pdb=" O VAL K 296 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1341 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: 4.79 Time building geometry restraints manager: 6.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3240 1.32 - 1.45: 4351 1.45 - 1.57: 9675 1.57 - 1.69: 3 1.69 - 1.81: 195 Bond restraints: 17464 Sorted by residual: bond pdb=" N ASN F 293 " pdb=" CA ASN F 293 " ideal model delta sigma weight residual 1.457 1.495 -0.039 1.53e-02 4.27e+03 6.40e+00 bond pdb=" C TYR B 289 " pdb=" O TYR B 289 " ideal model delta sigma weight residual 1.234 1.203 0.031 1.26e-02 6.30e+03 5.87e+00 bond pdb=" CA ASP I 290 " pdb=" CB ASP I 290 " ideal model delta sigma weight residual 1.530 1.494 0.036 1.51e-02 4.39e+03 5.63e+00 bond pdb=" CA PHE B 292 " pdb=" C PHE B 292 " ideal model delta sigma weight residual 1.523 1.557 -0.034 1.45e-02 4.76e+03 5.55e+00 bond pdb=" CA ASP B 290 " pdb=" CB ASP B 290 " ideal model delta sigma weight residual 1.531 1.493 0.038 1.69e-02 3.50e+03 5.07e+00 ... (remaining 17459 not shown) Histogram of bond angle deviations from ideal: 98.27 - 105.43: 213 105.43 - 112.60: 9124 112.60 - 119.76: 5865 119.76 - 126.92: 8217 126.92 - 134.09: 217 Bond angle restraints: 23636 Sorted by residual: angle pdb=" N ASN B 293 " pdb=" CA ASN B 293 " pdb=" C ASN B 293 " ideal model delta sigma weight residual 108.19 116.67 -8.48 1.29e+00 6.01e-01 4.33e+01 angle pdb=" N ARG J 219 " pdb=" CA ARG J 219 " pdb=" C ARG J 219 " ideal model delta sigma weight residual 112.38 120.30 -7.92 1.22e+00 6.72e-01 4.22e+01 angle pdb=" N ALA G 10 " pdb=" CA ALA G 10 " pdb=" C ALA G 10 " ideal model delta sigma weight residual 111.28 104.66 6.62 1.09e+00 8.42e-01 3.69e+01 angle pdb=" N ASN F 293 " pdb=" CA ASN F 293 " pdb=" C ASN F 293 " ideal model delta sigma weight residual 108.34 115.95 -7.61 1.31e+00 5.83e-01 3.38e+01 angle pdb=" N GLU G 17 " pdb=" CA GLU G 17 " pdb=" C GLU G 17 " ideal model delta sigma weight residual 111.36 117.12 -5.76 1.09e+00 8.42e-01 2.79e+01 ... (remaining 23631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 9534 16.96 - 33.93: 722 33.93 - 50.89: 155 50.89 - 67.86: 32 67.86 - 84.82: 18 Dihedral angle restraints: 10461 sinusoidal: 4057 harmonic: 6404 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 160.96 19.04 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA PHE B 151 " pdb=" C PHE B 151 " pdb=" N LEU B 152 " pdb=" CA LEU B 152 " ideal model delta harmonic sigma weight residual 180.00 162.43 17.57 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA PHE J 234 " pdb=" C PHE J 234 " pdb=" N PHE J 235 " pdb=" CA PHE J 235 " ideal model delta harmonic sigma weight residual 180.00 162.44 17.56 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 10458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1922 0.043 - 0.086: 529 0.086 - 0.129: 201 0.129 - 0.172: 23 0.172 - 0.215: 2 Chirality restraints: 2677 Sorted by residual: chirality pdb=" CA ARG J 219 " pdb=" N ARG J 219 " pdb=" C ARG J 219 " pdb=" CB ARG J 219 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA MET H 171 " pdb=" N MET H 171 " pdb=" C MET H 171 " pdb=" CB MET H 171 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE L 9 " pdb=" N ILE L 9 " pdb=" C ILE L 9 " pdb=" CB ILE L 9 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 ... (remaining 2674 not shown) Planarity restraints: 3060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER G 8 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C SER G 8 " 0.069 2.00e-02 2.50e+03 pdb=" O SER G 8 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE G 9 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP M 48 " 0.056 5.00e-02 4.00e+02 8.52e-02 1.16e+01 pdb=" N PRO M 49 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO M 49 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO M 49 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 235 " -0.014 2.00e-02 2.50e+03 1.92e-02 6.46e+00 pdb=" CG PHE K 235 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 PHE K 235 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE K 235 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 PHE K 235 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE K 235 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 235 " -0.000 2.00e-02 2.50e+03 ... (remaining 3057 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 465 2.69 - 3.25: 15786 3.25 - 3.80: 23756 3.80 - 4.35: 30461 4.35 - 4.90: 53275 Nonbonded interactions: 123743 Sorted by model distance: nonbonded pdb=" OE2 GLU J 260 " pdb=" OG1 THR J 263 " model vdw 2.142 2.440 nonbonded pdb=" O ALA F 56 " pdb=" OG SER F 334 " model vdw 2.147 2.440 nonbonded pdb=" O GLN D 170 " pdb=" OG1 THR D 174 " model vdw 2.165 2.440 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.203 2.440 nonbonded pdb=" OE2 GLU I 260 " pdb=" OG1 THR I 263 " model vdw 2.214 2.440 ... (remaining 123738 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' and (resid 153 through 187 or resid 198 through 211)) selection = chain 'C' selection = (chain 'D' and (resid 153 through 187 or resid 198 through 211)) selection = (chain 'E' and (resid 153 through 187 or resid 198 through 211)) selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'G' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } 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: 2.500 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: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 43.600 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 17464 Z= 0.250 Angle : 0.674 10.398 23636 Z= 0.383 Chirality : 0.046 0.215 2677 Planarity : 0.004 0.085 3060 Dihedral : 13.374 84.823 6307 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 0.16 % Allowed : 1.18 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.17), residues: 2180 helix: 0.85 (0.30), residues: 315 sheet: -1.10 (0.19), residues: 743 loop : -2.10 (0.16), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 63 HIS 0.006 0.001 HIS B 311 PHE 0.044 0.002 PHE K 235 TYR 0.035 0.002 TYR I 105 ARG 0.003 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 388 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 311 HIS cc_start: 0.6292 (m-70) cc_final: 0.5528 (m-70) outliers start: 3 outliers final: 1 residues processed: 389 average time/residue: 0.3926 time to fit residues: 212.6536 Evaluate side-chains 230 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 2.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 13 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 5.9990 chunk 161 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 108 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN B 142 HIS F 9 GLN F 44 GLN F 88 ASN ** F 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS F 237 ASN ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 18 GLN L 44 HIS A 162 GLN C 211 ASN ** I 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN N 44 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 17464 Z= 0.361 Angle : 0.693 9.464 23636 Z= 0.364 Chirality : 0.044 0.149 2677 Planarity : 0.005 0.091 3060 Dihedral : 5.002 57.329 2384 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.04 % Allowed : 13.12 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.17), residues: 2180 helix: 0.82 (0.29), residues: 309 sheet: -0.84 (0.19), residues: 714 loop : -2.05 (0.16), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 179 HIS 0.007 0.001 HIS H 156 PHE 0.017 0.002 PHE G 61 TYR 0.028 0.002 TYR J 111 ARG 0.006 0.000 ARG K 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 257 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 45 MET cc_start: 0.6804 (pmm) cc_final: 0.6348 (pmm) REVERT: L 21 MET cc_start: 0.7637 (tmm) cc_final: 0.7139 (tmm) REVERT: M 32 LYS cc_start: 0.9257 (pttt) cc_final: 0.8929 (pttt) REVERT: J 186 ASP cc_start: 0.6506 (t0) cc_final: 0.6290 (t0) outliers start: 38 outliers final: 25 residues processed: 274 average time/residue: 0.3754 time to fit residues: 141.8666 Evaluate side-chains 235 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 210 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain F residue 44 GLN Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 312 ASP Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 180 LYS Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain I residue 12 GLU Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain M residue 29 LYS Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 142 HIS Chi-restraints excluded: chain J residue 312 ASP Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 214 ARG Chi-restraints excluded: chain O residue 15 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 1.9990 chunk 60 optimal weight: 20.0000 chunk 160 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 193 optimal weight: 20.0000 chunk 209 optimal weight: 6.9990 chunk 172 optimal weight: 0.8980 chunk 192 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 HIS F 142 HIS ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** H 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17464 Z= 0.304 Angle : 0.654 12.768 23636 Z= 0.339 Chirality : 0.043 0.168 2677 Planarity : 0.004 0.057 3060 Dihedral : 4.835 56.718 2384 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.36 % Allowed : 15.59 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.17), residues: 2180 helix: 0.45 (0.28), residues: 321 sheet: -0.72 (0.20), residues: 716 loop : -1.90 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 179 HIS 0.007 0.001 HIS F 142 PHE 0.016 0.001 PHE K 241 TYR 0.024 0.001 TYR K 111 ARG 0.005 0.000 ARG K 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 MET cc_start: 0.7556 (tmm) cc_final: 0.7081 (tmm) REVERT: J 186 ASP cc_start: 0.6633 (t0) cc_final: 0.6357 (t0) outliers start: 44 outliers final: 31 residues processed: 258 average time/residue: 0.3739 time to fit residues: 133.6096 Evaluate side-chains 230 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 61 PHE Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 312 ASP Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 142 HIS Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 312 ASP Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain O residue 15 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 9.9990 chunk 145 optimal weight: 0.4980 chunk 100 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 205 optimal weight: 20.0000 chunk 101 optimal weight: 3.9990 chunk 184 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 88 ASN M 18 GLN ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 88 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17464 Z= 0.229 Angle : 0.618 9.088 23636 Z= 0.320 Chirality : 0.042 0.146 2677 Planarity : 0.004 0.050 3060 Dihedral : 4.609 56.186 2384 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.95 % Allowed : 16.60 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.17), residues: 2180 helix: 0.24 (0.28), residues: 323 sheet: -0.47 (0.20), residues: 714 loop : -1.82 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 339 HIS 0.010 0.001 HIS F 142 PHE 0.015 0.001 PHE K 241 TYR 0.016 0.001 TYR F 145 ARG 0.005 0.000 ARG J 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 238 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 12 GLU cc_start: 0.8887 (pp20) cc_final: 0.8583 (pp20) REVERT: L 21 MET cc_start: 0.7370 (tmm) cc_final: 0.6912 (tmm) REVERT: I 183 HIS cc_start: 0.7968 (OUTLIER) cc_final: 0.7663 (t70) REVERT: J 12 GLU cc_start: 0.8827 (pp20) cc_final: 0.8416 (pp20) outliers start: 55 outliers final: 37 residues processed: 268 average time/residue: 0.3685 time to fit residues: 137.1441 Evaluate side-chains 238 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 200 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 142 HIS Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 142 HIS Chi-restraints excluded: chain J residue 312 ASP Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 24 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 0.5980 chunk 116 optimal weight: 10.0000 chunk 2 optimal weight: 20.0000 chunk 153 optimal weight: 8.9990 chunk 84 optimal weight: 0.5980 chunk 175 optimal weight: 30.0000 chunk 142 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 105 optimal weight: 4.9990 chunk 184 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 142 HIS ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN I 36 ASN ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 88 ASN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17464 Z= 0.307 Angle : 0.650 9.100 23636 Z= 0.340 Chirality : 0.043 0.165 2677 Planarity : 0.004 0.056 3060 Dihedral : 4.663 55.980 2384 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.32 % Allowed : 18.05 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.17), residues: 2180 helix: -0.20 (0.27), residues: 334 sheet: -0.44 (0.20), residues: 716 loop : -1.85 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.004 0.001 HIS B 91 PHE 0.015 0.002 PHE K 241 TYR 0.008 0.001 TYR J 145 ARG 0.008 0.000 ARG J 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 219 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 GLU cc_start: 0.8979 (pp20) cc_final: 0.8688 (pp20) REVERT: L 21 MET cc_start: 0.7160 (tmm) cc_final: 0.6734 (tmm) REVERT: L 61 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7067 (m-10) REVERT: I 12 GLU cc_start: 0.8865 (pp20) cc_final: 0.8605 (pp20) REVERT: I 183 HIS cc_start: 0.8195 (OUTLIER) cc_final: 0.7930 (t70) REVERT: K 12 GLU cc_start: 0.8887 (pp20) cc_final: 0.8643 (pp20) outliers start: 62 outliers final: 46 residues processed: 251 average time/residue: 0.3703 time to fit residues: 129.9153 Evaluate side-chains 240 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 192 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 292 PHE Chi-restraints excluded: chain F residue 308 LEU Chi-restraints excluded: chain F residue 312 ASP Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 15 LEU Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain L residue 26 ASP Chi-restraints excluded: chain L residue 61 PHE Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 210 HIS Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain J residue 98 SER Chi-restraints excluded: chain J residue 119 ASN Chi-restraints excluded: chain J residue 142 HIS Chi-restraints excluded: chain J residue 312 ASP Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 157 ILE Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain O residue 15 LEU Chi-restraints excluded: chain O residue 24 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 40 optimal weight: 0.0470 chunk 120 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 95 optimal weight: 0.1980 chunk 17 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 GLN N 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17464 Z= 0.148 Angle : 0.621 9.600 23636 Z= 0.317 Chirality : 0.042 0.151 2677 Planarity : 0.004 0.054 3060 Dihedral : 4.326 55.088 2384 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.79 % Allowed : 19.39 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.17), residues: 2180 helix: -0.38 (0.27), residues: 334 sheet: 0.01 (0.20), residues: 679 loop : -1.86 (0.15), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 339 HIS 0.003 0.001 HIS A 156 PHE 0.014 0.001 PHE K 241 TYR 0.033 0.001 TYR K 145 ARG 0.009 0.000 ARG J 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 235 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 MET cc_start: 0.7279 (tmm) cc_final: 0.6938 (tmm) REVERT: I 183 HIS cc_start: 0.8067 (OUTLIER) cc_final: 0.7849 (t70) outliers start: 52 outliers final: 30 residues processed: 263 average time/residue: 0.3619 time to fit residues: 133.3685 Evaluate side-chains 223 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 192 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain E residue 175 MET Chi-restraints excluded: chain E residue 177 ASP Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain J residue 312 ASP Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 296 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 5.9990 chunk 23 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 150 optimal weight: 0.0570 chunk 116 optimal weight: 0.7980 chunk 173 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 205 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 125 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 overall best weight: 2.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.4838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17464 Z= 0.248 Angle : 0.678 15.850 23636 Z= 0.343 Chirality : 0.043 0.143 2677 Planarity : 0.004 0.052 3060 Dihedral : 4.424 55.371 2384 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.62 % Allowed : 20.67 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.17), residues: 2180 helix: -0.64 (0.27), residues: 334 sheet: 0.08 (0.20), residues: 681 loop : -1.89 (0.15), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.004 0.001 HIS C 156 PHE 0.014 0.001 PHE K 241 TYR 0.011 0.001 TYR I 289 ARG 0.009 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 214 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 MET cc_start: 0.7252 (tmm) cc_final: 0.6864 (tmm) REVERT: I 183 HIS cc_start: 0.8122 (OUTLIER) cc_final: 0.7888 (t70) outliers start: 49 outliers final: 37 residues processed: 241 average time/residue: 0.3723 time to fit residues: 125.7646 Evaluate side-chains 230 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 192 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 183 HIS Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 312 ASP Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 325 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 10.0000 chunk 81 optimal weight: 0.0070 chunk 122 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 40 optimal weight: 0.2980 chunk 39 optimal weight: 8.9990 chunk 130 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 161 optimal weight: 7.9990 overall best weight: 1.6604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.4964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17464 Z= 0.196 Angle : 0.676 14.260 23636 Z= 0.340 Chirality : 0.043 0.142 2677 Planarity : 0.004 0.053 3060 Dihedral : 4.322 55.540 2384 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.52 % Allowed : 20.84 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.17), residues: 2180 helix: -0.79 (0.27), residues: 334 sheet: 0.07 (0.20), residues: 691 loop : -1.82 (0.16), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS G 44 PHE 0.014 0.001 PHE K 241 TYR 0.012 0.001 TYR I 289 ARG 0.008 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 213 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 MET cc_start: 0.7228 (tmm) cc_final: 0.6848 (tmm) outliers start: 47 outliers final: 40 residues processed: 240 average time/residue: 0.3639 time to fit residues: 121.9331 Evaluate side-chains 237 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 142 HIS Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain J residue 223 THR Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 312 ASP Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 325 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 4.9990 chunk 196 optimal weight: 0.2980 chunk 179 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 83 optimal weight: 0.0570 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 180 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 overall best weight: 3.0704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17464 Z= 0.285 Angle : 0.711 13.623 23636 Z= 0.362 Chirality : 0.043 0.173 2677 Planarity : 0.004 0.053 3060 Dihedral : 4.515 56.422 2384 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.52 % Allowed : 21.10 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.17), residues: 2180 helix: -0.88 (0.28), residues: 334 sheet: -0.21 (0.19), residues: 747 loop : -1.71 (0.16), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.004 0.001 HIS C 156 PHE 0.014 0.001 PHE K 241 TYR 0.010 0.001 TYR I 289 ARG 0.010 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 207 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 GLU cc_start: 0.7964 (mp0) cc_final: 0.7657 (pm20) REVERT: L 21 MET cc_start: 0.7224 (tmm) cc_final: 0.6914 (tmm) REVERT: L 47 GLU cc_start: 0.8021 (mp0) cc_final: 0.7669 (pm20) REVERT: J 12 GLU cc_start: 0.8834 (pp20) cc_final: 0.8539 (pp20) outliers start: 47 outliers final: 43 residues processed: 236 average time/residue: 0.3767 time to fit residues: 123.7445 Evaluate side-chains 236 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 193 time to evaluate : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 168 LEU Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain E residue 187 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 312 ASP Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain N residue 24 ASN Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 10.0000 chunk 202 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 140 optimal weight: 30.0000 chunk 212 optimal weight: 6.9990 chunk 195 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 103 optimal weight: 0.0040 overall best weight: 1.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17464 Z= 0.208 Angle : 0.722 14.532 23636 Z= 0.363 Chirality : 0.043 0.210 2677 Planarity : 0.004 0.054 3060 Dihedral : 4.394 56.093 2384 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.36 % Allowed : 21.48 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.17), residues: 2180 helix: -1.10 (0.27), residues: 334 sheet: 0.07 (0.20), residues: 712 loop : -1.75 (0.16), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.003 0.001 HIS C 156 PHE 0.014 0.001 PHE K 241 TYR 0.011 0.001 TYR I 289 ARG 0.013 0.000 ARG G 13 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4360 Ramachandran restraints generated. 2180 Oldfield, 0 Emsley, 2180 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 216 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 47 GLU cc_start: 0.8050 (mp0) cc_final: 0.7732 (pm20) REVERT: L 18 GLN cc_start: 0.8529 (tp40) cc_final: 0.8135 (tp40) REVERT: L 21 MET cc_start: 0.7261 (tmm) cc_final: 0.6847 (tmm) REVERT: L 47 GLU cc_start: 0.7960 (mp0) cc_final: 0.7630 (pm20) REVERT: N 47 GLU cc_start: 0.7653 (mp0) cc_final: 0.7450 (pm20) outliers start: 44 outliers final: 38 residues processed: 244 average time/residue: 0.3503 time to fit residues: 119.4698 Evaluate side-chains 244 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 206 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain F residue 10 GLU Chi-restraints excluded: chain F residue 98 SER Chi-restraints excluded: chain F residue 101 MET Chi-restraints excluded: chain F residue 135 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain F residue 296 VAL Chi-restraints excluded: chain F residue 338 ILE Chi-restraints excluded: chain L residue 24 ASN Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 187 ILE Chi-restraints excluded: chain H residue 175 MET Chi-restraints excluded: chain H residue 177 ASP Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 223 THR Chi-restraints excluded: chain I residue 270 ILE Chi-restraints excluded: chain I residue 296 VAL Chi-restraints excluded: chain I residue 312 ASP Chi-restraints excluded: chain M residue 13 ARG Chi-restraints excluded: chain J residue 296 VAL Chi-restraints excluded: chain J residue 312 ASP Chi-restraints excluded: chain J residue 338 ILE Chi-restraints excluded: chain J residue 339 TRP Chi-restraints excluded: chain N residue 13 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 223 THR Chi-restraints excluded: chain K residue 294 CYS Chi-restraints excluded: chain K residue 296 VAL Chi-restraints excluded: chain K residue 325 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 51 optimal weight: 0.0870 chunk 155 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 173 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.072430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.044590 restraints weight = 78820.640| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 5.38 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17464 Z= 0.359 Angle : 0.790 18.851 23636 Z= 0.401 Chirality : 0.044 0.194 2677 Planarity : 0.004 0.054 3060 Dihedral : 4.746 57.167 2384 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.30 % Allowed : 22.07 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.17), residues: 2180 helix: -1.20 (0.27), residues: 334 sheet: -0.20 (0.19), residues: 747 loop : -1.73 (0.16), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 179 HIS 0.005 0.001 HIS C 156 PHE 0.015 0.001 PHE F 292 TYR 0.010 0.001 TYR F 105 ARG 0.013 0.000 ARG G 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3851.12 seconds wall clock time: 69 minutes 39.82 seconds (4179.82 seconds total)