Starting phenix.real_space_refine (version: 1.21rc1) on Tue Aug 15 00:24:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkb_36367/08_2023/8jkb_36367.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkb_36367/08_2023/8jkb_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_36367/08_2023/8jkb_36367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkb_36367/08_2023/8jkb_36367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkb_36367/08_2023/8jkb_36367.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jkb_36367/08_2023/8jkb_36367.pdb" } 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-1.21rc1-5044/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: 8.73, per 1000 atoms: 0.51 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: 6.42 Conformation dependent library (CDL) restraints added in 2.6 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: 1.82 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: 5.46 Time building geometry restraints manager: 6.85 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: 3.050 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: 0.010 Extract box with map and model: 10.210 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 44.490 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.550 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.135 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 outliers start: 3 outliers final: 1 residues processed: 389 average time/residue: 0.3973 time to fit residues: 213.4789 Evaluate side-chains 230 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 2.121 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.7046 time to fit residues: 3.7818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN F 88 ASN F 91 HIS 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: 0.7391 moved from start: 0.3140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 17464 Z= 0.363 Angle : 0.692 8.888 23636 Z= 0.365 Chirality : 0.044 0.142 2677 Planarity : 0.005 0.095 3060 Dihedral : 4.869 18.001 2380 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 1.98 % 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: -1.81 (0.17), residues: 2180 helix: 0.76 (0.29), residues: 309 sheet: -0.83 (0.19), residues: 714 loop : -2.04 (0.16), residues: 1157 *********************** 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 294 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 257 time to evaluate : 2.080 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: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 274 average time/residue: 0.3906 time to fit residues: 147.5623 Evaluate side-chains 235 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 212 time to evaluate : 2.165 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2063 time to fit residues: 10.6126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 131 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 7.9990 chunk 209 optimal weight: 0.2980 chunk 172 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 overall best weight: 3.0588 ------------------------------------------------------------------------------- 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 9 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS ** J 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 17464 Z= 0.279 Angle : 0.632 12.775 23636 Z= 0.326 Chirality : 0.043 0.175 2677 Planarity : 0.004 0.058 3060 Dihedral : 4.600 18.253 2380 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 1.34 % 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: -1.64 (0.17), residues: 2180 helix: 0.55 (0.28), residues: 321 sheet: -0.67 (0.20), residues: 716 loop : -1.88 (0.16), residues: 1143 *********************** 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 261 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 236 time to evaluate : 2.096 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 outliers start: 25 outliers final: 14 residues processed: 254 average time/residue: 0.3916 time to fit residues: 137.3506 Evaluate side-chains 210 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 2.053 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1878 time to fit residues: 7.1855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 5.9990 chunk 145 optimal weight: 0.0070 chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 130 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 205 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 55 optimal weight: 0.0980 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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** L 44 HIS I 88 ASN M 18 GLN J 9 GLN ** N 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 ASN K 88 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 17464 Z= 0.163 Angle : 0.599 9.676 23636 Z= 0.307 Chirality : 0.042 0.169 2677 Planarity : 0.004 0.052 3060 Dihedral : 4.235 15.706 2380 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 1.45 % 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: -1.49 (0.17), residues: 2180 helix: 0.24 (0.29), residues: 316 sheet: -0.19 (0.20), residues: 679 loop : -1.87 (0.16), residues: 1185 *********************** 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 274 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 247 time to evaluate : 1.990 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 outliers start: 27 outliers final: 8 residues processed: 260 average time/residue: 0.3876 time to fit residues: 139.3384 Evaluate side-chains 210 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 202 time to evaluate : 2.099 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1678 time to fit residues: 5.2405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 9.9990 chunk 116 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 chunk 153 optimal weight: 10.0000 chunk 84 optimal weight: 3.9990 chunk 175 optimal weight: 30.0000 chunk 142 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 105 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 G 18 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 HIS J 88 ASN J 119 ASN N 18 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.4418 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= 0.275 Angle : 0.642 12.022 23636 Z= 0.332 Chirality : 0.043 0.143 2677 Planarity : 0.004 0.057 3060 Dihedral : 4.374 16.732 2380 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 1.61 % 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: -0.07 (0.28), residues: 328 sheet: -0.35 (0.20), residues: 718 loop : -1.78 (0.16), residues: 1134 *********************** 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 252 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 2.204 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 outliers start: 30 outliers final: 16 residues processed: 236 average time/residue: 0.3895 time to fit residues: 127.6613 Evaluate side-chains 211 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 1.972 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2357 time to fit residues: 8.7113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 40 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 206 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 17464 Z= 0.273 Angle : 0.649 9.340 23636 Z= 0.335 Chirality : 0.042 0.167 2677 Planarity : 0.004 0.049 3060 Dihedral : 4.376 17.549 2380 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 1.34 % 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: -1.62 (0.17), residues: 2180 helix: -0.49 (0.27), residues: 334 sheet: -0.30 (0.20), residues: 716 loop : -1.80 (0.16), residues: 1130 *********************** 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 245 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 220 time to evaluate : 1.978 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 outliers start: 25 outliers final: 15 residues processed: 236 average time/residue: 0.3760 time to fit residues: 124.1202 Evaluate side-chains 205 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 190 time to evaluate : 2.104 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1532 time to fit residues: 6.9898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 117 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 chunk 205 optimal weight: 30.0000 chunk 128 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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** G 18 GLN ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 36 ASN I 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.046 17464 Z= 0.399 Angle : 0.724 10.021 23636 Z= 0.377 Chirality : 0.044 0.144 2677 Planarity : 0.004 0.057 3060 Dihedral : 4.697 19.204 2380 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer Outliers : 1.66 % 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: -1.79 (0.16), residues: 2180 helix: -0.75 (0.26), residues: 334 sheet: -0.42 (0.19), residues: 741 loop : -1.88 (0.16), residues: 1105 *********************** 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 234 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 1.967 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 outliers start: 31 outliers final: 15 residues processed: 219 average time/residue: 0.3831 time to fit residues: 117.5961 Evaluate side-chains 204 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 189 time to evaluate : 2.211 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1481 time to fit residues: 6.9289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 0.3980 chunk 61 optimal weight: 5.9990 chunk 40 optimal weight: 30.0000 chunk 39 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 161 optimal weight: 6.9990 overall best weight: 3.6788 ------------------------------------------------------------------------------- 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: 0.7489 moved from start: 0.5144 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= 0.327 Angle : 0.718 15.273 23636 Z= 0.367 Chirality : 0.043 0.154 2677 Planarity : 0.004 0.053 3060 Dihedral : 4.605 19.833 2380 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer Outliers : 0.70 % 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: -1.78 (0.17), residues: 2180 helix: -0.86 (0.26), residues: 334 sheet: -0.36 (0.19), residues: 741 loop : -1.87 (0.16), residues: 1105 *********************** 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 216 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 203 time to evaluate : 1.930 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 outliers start: 13 outliers final: 7 residues processed: 209 average time/residue: 0.3938 time to fit residues: 114.0567 Evaluate side-chains 193 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 2.085 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1536 time to fit residues: 4.7495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 3.9990 chunk 196 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 191 optimal weight: 20.0000 chunk 115 optimal weight: 8.9990 chunk 83 optimal weight: 0.8980 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 chunk 180 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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** ** 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: 0.7414 moved from start: 0.5254 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= 0.190 Angle : 0.706 14.957 23636 Z= 0.355 Chirality : 0.043 0.178 2677 Planarity : 0.004 0.054 3060 Dihedral : 4.317 19.144 2380 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 0.48 % 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: -1.58 (0.17), residues: 2180 helix: -0.84 (0.27), residues: 334 sheet: 0.08 (0.20), residues: 706 loop : -1.89 (0.16), residues: 1140 *********************** 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 227 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 218 time to evaluate : 2.131 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 outliers start: 9 outliers final: 5 residues processed: 223 average time/residue: 0.4020 time to fit residues: 125.3267 Evaluate side-chains 201 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 196 time to evaluate : 2.130 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1832 time to fit residues: 4.4865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 5.9990 chunk 202 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 140 optimal weight: 30.0000 chunk 212 optimal weight: 5.9990 chunk 195 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 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** ** F 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5407 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= 0.358 Angle : 0.774 14.048 23636 Z= 0.395 Chirality : 0.044 0.250 2677 Planarity : 0.004 0.053 3060 Dihedral : 4.570 18.553 2380 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 0.54 % 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: -1.76 (0.16), residues: 2180 helix: -1.15 (0.26), residues: 334 sheet: -0.22 (0.19), residues: 737 loop : -1.86 (0.16), residues: 1109 ********************** 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 214 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 204 time to evaluate : 2.307 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 outliers start: 10 outliers final: 8 residues processed: 206 average time/residue: 0.4040 time to fit residues: 115.7720 Evaluate side-chains 204 residues out of total 1867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 2.062 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2350 time to fit residues: 5.6917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 51 optimal weight: 4.9990 chunk 155 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 46 optimal weight: 0.1980 chunk 169 optimal weight: 4.9990 chunk 70 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 21 optimal weight: 0.0470 chunk 31 optimal weight: 0.9980 overall best weight: 2.2482 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.073320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.045511 restraints weight = 77938.294| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 5.33 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 17464 Z= 0.239 Angle : 0.744 14.894 23636 Z= 0.374 Chirality : 0.044 0.229 2677 Planarity : 0.004 0.053 3060 Dihedral : 4.390 18.850 2380 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.32 % 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: -1.64 (0.17), residues: 2180 helix: -1.11 (0.27), residues: 332 sheet: 0.10 (0.20), residues: 702 loop : -1.89 (0.15), residues: 1146 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3709.19 seconds wall clock time: 68 minutes 21.02 seconds (4101.02 seconds total)