Starting phenix.real_space_refine on Tue Nov 21 09:23:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozf_17307/11_2023/8ozf_17307_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozf_17307/11_2023/8ozf_17307.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozf_17307/11_2023/8ozf_17307.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozf_17307/11_2023/8ozf_17307.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozf_17307/11_2023/8ozf_17307_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ozf_17307/11_2023/8ozf_17307_updated.pdb" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1220 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 136 5.49 5 S 96 5.16 5 C 20266 2.51 5 N 5310 2.21 5 O 6268 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 13": "OD1" <-> "OD2" Residue "A ASP 14": "OD1" <-> "OD2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 136": "OE1" <-> "OE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 79": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 55": "OD1" <-> "OD2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 87": "OE1" <-> "OE2" Residue "E PHE 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 233": "OD1" <-> "OD2" Residue "E ASP 273": "OD1" <-> "OD2" Residue "E PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 356": "OE1" <-> "OE2" Residue "E PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 369": "OE1" <-> "OE2" Residue "E TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 13": "OD1" <-> "OD2" Residue "F PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 101": "OE1" <-> "OE2" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 136": "OE1" <-> "OE2" Residue "F TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 168": "OE1" <-> "OE2" Residue "F PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F GLU 284": "OE1" <-> "OE2" Residue "F TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 306": "OE1" <-> "OE2" Residue "F PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 8": "OE1" <-> "OE2" Residue "G TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 79": "OE1" <-> "OE2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 87": "OE1" <-> "OE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 226": "OE1" <-> "OE2" Residue "G TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 331": "OE1" <-> "OE2" Residue "G PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 415": "OE1" <-> "OE2" Residue "G ASP 474": "OD1" <-> "OD2" Residue "G ASP 495": "OD1" <-> "OD2" Residue "G TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 40": "OD1" <-> "OD2" Residue "H GLU 72": "OE1" <-> "OE2" Residue "H TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 119": "OD1" <-> "OD2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 166": "OE1" <-> "OE2" Residue "H TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 231": "OE1" <-> "OE2" Residue "H TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 316": "OD1" <-> "OD2" Residue "H TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 394": "OE1" <-> "OE2" Residue "H GLU 398": "OE1" <-> "OE2" Residue "H PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M ASP 100": "OD1" <-> "OD2" Residue "M GLU 134": "OE1" <-> "OE2" Residue "M PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 146": "OE1" <-> "OE2" Residue "M TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 400": "OE1" <-> "OE2" Residue "M TYR 403": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 444": "OE1" <-> "OE2" Residue "M GLU 449": "OE1" <-> "OE2" Residue "M PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 32076 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "C" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "E" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "F" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "G" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "H" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3486 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 11, 'TRANS': 406} Chain breaks: 1 Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "J" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "L" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "M" Number of atoms: 3821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 473, 3821 Classifications: {'peptide': 473} Link IDs: {'PTRANS': 24, 'TRANS': 448} Chain breaks: 1 Chain: "N" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "O" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 361 Classifications: {'RNA': 18} Modifications used: {'p5*END': 1, 'rna2p_pyr': 1, 'rna3p_pyr': 17} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "P" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "Q" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 333 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'AR6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.89, per 1000 atoms: 0.53 Number of scatterers: 32076 At special positions: 0 Unit cell: (177.87, 206.91, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 P 136 15.00 O 6268 8.00 N 5310 7.00 C 20266 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: 13.62 Conformation dependent library (CDL) restraints added in 5.8 seconds 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6792 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 36 sheets defined 33.5% alpha, 13.4% beta 22 base pairs and 95 stacking pairs defined. Time for finding SS restraints: 14.19 Creating SS restraints... Processing helix chain 'A' and resid 15 through 28 removed outlier: 3.508A pdb=" N GLY A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.905A pdb=" N GLU A 50 " --> pdb=" O TRP A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 88 Processing helix chain 'A' and resid 105 through 107 No H-bonds generated for 'chain 'A' and resid 105 through 107' Processing helix chain 'A' and resid 124 through 137 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 220 through 223 removed outlier: 4.422A pdb=" N PHE A 223 " --> pdb=" O ALA A 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 228 through 232 removed outlier: 4.000A pdb=" N THR A 232 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 258 through 279 removed outlier: 3.702A pdb=" N ARG A 263 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 265 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 303 No H-bonds generated for 'chain 'A' and resid 301 through 303' Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 370 through 383 removed outlier: 4.319A pdb=" N THR A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 17 No H-bonds generated for 'chain 'B' and resid 15 through 17' Processing helix chain 'B' and resid 23 through 30 Processing helix chain 'B' and resid 47 through 61 removed outlier: 3.584A pdb=" N LYS B 51 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 81 No H-bonds generated for 'chain 'B' and resid 78 through 81' Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.835A pdb=" N PHE B 104 " --> pdb=" O ASP B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 131 removed outlier: 3.607A pdb=" N PHE B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LYS B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 206 through 213 Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 249 through 264 removed outlier: 3.676A pdb=" N ALA B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 350 removed outlier: 4.369A pdb=" N GLN B 349 " --> pdb=" O SER B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 376 removed outlier: 3.555A pdb=" N VAL B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 464 removed outlier: 3.973A pdb=" N LEU B 460 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 490 Processing helix chain 'B' and resid 503 through 505 No H-bonds generated for 'chain 'B' and resid 503 through 505' Processing helix chain 'C' and resid 11 through 27 removed outlier: 3.734A pdb=" N ASN C 15 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ASP C 16 " --> pdb=" O PRO C 12 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N PHE C 17 " --> pdb=" O ASP C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 66 through 69 No H-bonds generated for 'chain 'C' and resid 66 through 69' Processing helix chain 'C' and resid 72 through 88 Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 124 through 138 removed outlier: 3.694A pdb=" N LEU C 128 " --> pdb=" O TRP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 157 Processing helix chain 'C' and resid 191 through 193 No H-bonds generated for 'chain 'C' and resid 191 through 193' Processing helix chain 'C' and resid 200 through 202 No H-bonds generated for 'chain 'C' and resid 200 through 202' Processing helix chain 'C' and resid 228 through 230 No H-bonds generated for 'chain 'C' and resid 228 through 230' Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 243 through 248 Processing helix chain 'C' and resid 258 through 279 removed outlier: 3.518A pdb=" N LYS C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE C 265 " --> pdb=" O CYS C 261 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL C 266 " --> pdb=" O LYS C 262 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN C 267 " --> pdb=" O ARG C 263 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 268 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 365 Processing helix chain 'C' and resid 370 through 384 removed outlier: 3.848A pdb=" N THR C 375 " --> pdb=" O ASN C 371 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N LYS C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 17 No H-bonds generated for 'chain 'E' and resid 15 through 17' Processing helix chain 'E' and resid 23 through 30 Processing helix chain 'E' and resid 47 through 61 removed outlier: 3.608A pdb=" N LYS E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE E 52 " --> pdb=" O GLN E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 81 No H-bonds generated for 'chain 'E' and resid 78 through 81' Processing helix chain 'E' and resid 100 through 103 No H-bonds generated for 'chain 'E' and resid 100 through 103' Processing helix chain 'E' and resid 110 through 131 removed outlier: 3.763A pdb=" N LYS E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 150 Processing helix chain 'E' and resid 206 through 217 removed outlier: 4.243A pdb=" N LEU E 215 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS E 216 " --> pdb=" O ALA E 212 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N HIS E 217 " --> pdb=" O ARG E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 233 No H-bonds generated for 'chain 'E' and resid 231 through 233' Processing helix chain 'E' and resid 249 through 263 Processing helix chain 'E' and resid 332 through 350 removed outlier: 3.637A pdb=" N TYR E 346 " --> pdb=" O SER E 342 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN E 349 " --> pdb=" O SER E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 376 removed outlier: 3.510A pdb=" N VAL E 376 " --> pdb=" O ALA E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 429 No H-bonds generated for 'chain 'E' and resid 427 through 429' Processing helix chain 'E' and resid 452 through 464 removed outlier: 3.739A pdb=" N LEU E 460 " --> pdb=" O LEU E 456 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N SER E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LYS E 464 " --> pdb=" O LEU E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 478 through 490 removed outlier: 3.766A pdb=" N ASP E 484 " --> pdb=" O LEU E 480 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 505 No H-bonds generated for 'chain 'E' and resid 503 through 505' Processing helix chain 'F' and resid 15 through 28 Processing helix chain 'F' and resid 44 through 55 removed outlier: 3.560A pdb=" N GLU F 50 " --> pdb=" O TRP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 70 No H-bonds generated for 'chain 'F' and resid 68 through 70' Processing helix chain 'F' and resid 72 through 88 Processing helix chain 'F' and resid 105 through 107 No H-bonds generated for 'chain 'F' and resid 105 through 107' Processing helix chain 'F' and resid 110 through 113 No H-bonds generated for 'chain 'F' and resid 110 through 113' Processing helix chain 'F' and resid 124 through 137 Processing helix chain 'F' and resid 147 through 157 Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'F' and resid 200 through 202 No H-bonds generated for 'chain 'F' and resid 200 through 202' Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.716A pdb=" N GLU F 231 " --> pdb=" O PRO F 228 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR F 232 " --> pdb=" O LYS F 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 228 through 232' Processing helix chain 'F' and resid 235 through 237 No H-bonds generated for 'chain 'F' and resid 235 through 237' Processing helix chain 'F' and resid 243 through 248 Processing helix chain 'F' and resid 258 through 279 removed outlier: 3.744A pdb=" N ARG F 263 " --> pdb=" O ALA F 259 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL F 266 " --> pdb=" O LYS F 262 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN F 267 " --> pdb=" O ARG F 263 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU F 268 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 303 No H-bonds generated for 'chain 'F' and resid 301 through 303' Processing helix chain 'F' and resid 354 through 367 removed outlier: 4.769A pdb=" N ASN F 367 " --> pdb=" O ARG F 363 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 383 removed outlier: 3.747A pdb=" N THR F 375 " --> pdb=" O ASN F 371 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS F 376 " --> pdb=" O THR F 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 17 No H-bonds generated for 'chain 'G' and resid 15 through 17' Processing helix chain 'G' and resid 24 through 30 Processing helix chain 'G' and resid 47 through 61 removed outlier: 3.932A pdb=" N LYS G 51 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE G 52 " --> pdb=" O GLN G 48 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE G 53 " --> pdb=" O GLY G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 82 Processing helix chain 'G' and resid 98 through 105 removed outlier: 3.793A pdb=" N PHE G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 110 through 131 Processing helix chain 'G' and resid 146 through 149 No H-bonds generated for 'chain 'G' and resid 146 through 149' Processing helix chain 'G' and resid 159 through 161 No H-bonds generated for 'chain 'G' and resid 159 through 161' Processing helix chain 'G' and resid 206 through 213 Processing helix chain 'G' and resid 215 through 217 No H-bonds generated for 'chain 'G' and resid 215 through 217' Processing helix chain 'G' and resid 231 through 233 No H-bonds generated for 'chain 'G' and resid 231 through 233' Processing helix chain 'G' and resid 249 through 263 removed outlier: 3.781A pdb=" N ALA G 259 " --> pdb=" O THR G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 350 removed outlier: 3.695A pdb=" N TYR G 346 " --> pdb=" O SER G 342 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLN G 349 " --> pdb=" O SER G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 376 removed outlier: 3.691A pdb=" N ALA G 372 " --> pdb=" O GLN G 368 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 376 " --> pdb=" O ALA G 372 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 464 removed outlier: 3.818A pdb=" N SER G 461 " --> pdb=" O LYS G 457 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LYS G 464 " --> pdb=" O LEU G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 478 through 490 Processing helix chain 'G' and resid 503 through 505 No H-bonds generated for 'chain 'G' and resid 503 through 505' Processing helix chain 'H' and resid 15 through 27 Processing helix chain 'H' and resid 45 through 55 Processing helix chain 'H' and resid 72 through 88 Processing helix chain 'H' and resid 110 through 113 No H-bonds generated for 'chain 'H' and resid 110 through 113' Processing helix chain 'H' and resid 124 through 137 removed outlier: 3.600A pdb=" N LEU H 128 " --> pdb=" O TRP H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 157 Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 228 through 232 removed outlier: 3.575A pdb=" N THR H 232 " --> pdb=" O LYS H 229 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 237 No H-bonds generated for 'chain 'H' and resid 235 through 237' Processing helix chain 'H' and resid 243 through 248 Processing helix chain 'H' and resid 258 through 280 removed outlier: 3.722A pdb=" N ARG H 263 " --> pdb=" O ALA H 259 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE H 265 " --> pdb=" O CYS H 261 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN H 267 " --> pdb=" O ARG H 263 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU H 268 " --> pdb=" O LEU H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 303 No H-bonds generated for 'chain 'H' and resid 301 through 303' Processing helix chain 'H' and resid 354 through 367 removed outlier: 4.993A pdb=" N ASN H 367 " --> pdb=" O ARG H 363 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 384 removed outlier: 4.160A pdb=" N THR H 375 " --> pdb=" O ASN H 371 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LYS H 376 " --> pdb=" O THR H 372 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 24 through 29 Processing helix chain 'M' and resid 47 through 61 removed outlier: 4.117A pdb=" N ILE M 52 " --> pdb=" O GLN M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 78 through 82 Processing helix chain 'M' and resid 98 through 105 removed outlier: 3.666A pdb=" N PHE M 104 " --> pdb=" O ASP M 100 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 130 removed outlier: 3.649A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 149 Processing helix chain 'M' and resid 159 through 161 No H-bonds generated for 'chain 'M' and resid 159 through 161' Processing helix chain 'M' and resid 206 through 213 Processing helix chain 'M' and resid 231 through 233 No H-bonds generated for 'chain 'M' and resid 231 through 233' Processing helix chain 'M' and resid 249 through 263 Processing helix chain 'M' and resid 332 through 350 removed outlier: 4.963A pdb=" N GLN M 349 " --> pdb=" O SER M 345 " (cutoff:3.500A) Processing helix chain 'M' and resid 367 through 376 Processing helix chain 'M' and resid 427 through 429 No H-bonds generated for 'chain 'M' and resid 427 through 429' Processing helix chain 'M' and resid 452 through 464 removed outlier: 3.809A pdb=" N LEU M 460 " --> pdb=" O LEU M 456 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER M 461 " --> pdb=" O LYS M 457 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LYS M 464 " --> pdb=" O LEU M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 490 Processing helix chain 'M' and resid 503 through 505 No H-bonds generated for 'chain 'M' and resid 503 through 505' Processing sheet with id= A, first strand: chain 'A' and resid 169 through 172 Processing sheet with id= B, first strand: chain 'A' and resid 175 through 177 Processing sheet with id= C, first strand: chain 'A' and resid 186 through 188 Processing sheet with id= D, first strand: chain 'A' and resid 283 through 286 Processing sheet with id= E, first strand: chain 'A' and resid 390 through 394 Processing sheet with id= F, first strand: chain 'A' and resid 4 through 8 removed outlier: 7.507A pdb=" N PHE A 6 " --> pdb=" O CYS A 58 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE A 60 " --> pdb=" O PHE A 6 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N SER A 8 " --> pdb=" O PHE A 60 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LEU A 62 " --> pdb=" O SER A 8 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 92 through 95 removed outlier: 6.447A pdb=" N VAL B 138 " --> pdb=" O GLY B 42 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N ILE B 44 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE B 140 " --> pdb=" O ILE B 44 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N VAL B 141 " --> pdb=" O PRO B 220 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLN B 222 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL B 143 " --> pdb=" O GLN B 222 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N PHE B 224 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 284 through 286 Processing sheet with id= I, first strand: chain 'B' and resid 356 through 361 removed outlier: 6.936A pdb=" N ASN B 382 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE B 359 " --> pdb=" O ASN B 382 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 384 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ALA B 361 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL B 386 " --> pdb=" O ALA B 361 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR B 387 " --> pdb=" O ILE B 445 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE B 445 " --> pdb=" O THR B 387 " (cutoff:3.500A) removed outlier: 7.560A pdb=" N SER B 389 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ILE B 443 " --> pdb=" O SER B 389 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE B 419 " --> pdb=" O VAL B 412 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL B 412 " --> pdb=" O PHE B 419 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 117 through 119 removed outlier: 8.329A pdb=" N ILE C 118 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N ILE C 95 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE C 60 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N LEU C 97 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N LEU C 62 " --> pdb=" O LEU C 97 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS C 4 " --> pdb=" O CYS C 58 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N PHE C 60 " --> pdb=" O LYS C 4 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE C 6 " --> pdb=" O PHE C 60 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LEU C 62 " --> pdb=" O PHE C 6 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER C 8 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N SER C 64 " --> pdb=" O SER C 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 169 through 172 Processing sheet with id= L, first strand: chain 'C' and resid 175 through 177 Processing sheet with id= M, first strand: chain 'C' and resid 186 through 188 Processing sheet with id= N, first strand: chain 'C' and resid 283 through 285 Processing sheet with id= O, first strand: chain 'C' and resid 390 through 394 Processing sheet with id= P, first strand: chain 'E' and resid 92 through 95 removed outlier: 6.446A pdb=" N VAL E 138 " --> pdb=" O GLY E 42 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N ILE E 44 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N PHE E 140 " --> pdb=" O ILE E 44 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 282 through 286 Processing sheet with id= R, first strand: chain 'E' and resid 356 through 361 removed outlier: 6.659A pdb=" N ASN E 382 " --> pdb=" O VAL E 357 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N ILE E 359 " --> pdb=" O ASN E 382 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N VAL E 384 " --> pdb=" O ILE E 359 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ALA E 361 " --> pdb=" O VAL E 384 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL E 386 " --> pdb=" O ALA E 361 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR E 387 " --> pdb=" O ILE E 445 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE E 445 " --> pdb=" O THR E 387 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N SER E 389 " --> pdb=" O ILE E 443 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ILE E 443 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE E 419 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N VAL E 412 " --> pdb=" O PHE E 419 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 94 through 98 removed outlier: 8.776A pdb=" N ILE F 95 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N PHE F 60 " --> pdb=" O ILE F 95 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU F 97 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU F 62 " --> pdb=" O LEU F 97 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N LYS F 4 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE F 60 " --> pdb=" O LYS F 4 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE F 6 " --> pdb=" O PHE F 60 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N LEU F 62 " --> pdb=" O PHE F 6 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N SER F 8 " --> pdb=" O LEU F 62 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N SER F 64 " --> pdb=" O SER F 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'F' and resid 169 through 172 Processing sheet with id= U, first strand: chain 'F' and resid 175 through 177 Processing sheet with id= V, first strand: chain 'F' and resid 186 through 188 Processing sheet with id= W, first strand: chain 'F' and resid 283 through 286 Processing sheet with id= X, first strand: chain 'F' and resid 390 through 394 Processing sheet with id= Y, first strand: chain 'G' and resid 92 through 95 removed outlier: 6.192A pdb=" N VAL G 138 " --> pdb=" O GLY G 42 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE G 44 " --> pdb=" O VAL G 138 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N PHE G 140 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL G 141 " --> pdb=" O PRO G 220 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLN G 222 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VAL G 143 " --> pdb=" O GLN G 222 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N PHE G 224 " --> pdb=" O VAL G 143 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 282 through 286 Processing sheet with id= AA, first strand: chain 'G' and resid 356 through 361 removed outlier: 6.332A pdb=" N ASN G 382 " --> pdb=" O VAL G 357 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE G 359 " --> pdb=" O ASN G 382 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL G 384 " --> pdb=" O ILE G 359 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ALA G 361 " --> pdb=" O VAL G 384 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL G 386 " --> pdb=" O ALA G 361 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N THR G 387 " --> pdb=" O ILE G 445 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ILE G 445 " --> pdb=" O THR G 387 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N SER G 389 " --> pdb=" O ILE G 443 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ILE G 443 " --> pdb=" O SER G 389 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE G 419 " --> pdb=" O VAL G 412 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL G 412 " --> pdb=" O PHE G 419 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 94 through 98 removed outlier: 8.856A pdb=" N ILE H 95 " --> pdb=" O CYS H 58 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N PHE H 60 " --> pdb=" O ILE H 95 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU H 97 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU H 62 " --> pdb=" O LEU H 97 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N LYS H 4 " --> pdb=" O CYS H 58 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N PHE H 60 " --> pdb=" O LYS H 4 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N PHE H 6 " --> pdb=" O PHE H 60 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU H 62 " --> pdb=" O PHE H 6 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER H 8 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N SER H 64 " --> pdb=" O SER H 8 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'H' and resid 169 through 172 Processing sheet with id= AD, first strand: chain 'H' and resid 175 through 177 Processing sheet with id= AE, first strand: chain 'H' and resid 186 through 188 Processing sheet with id= AF, first strand: chain 'H' and resid 283 through 286 Processing sheet with id= AG, first strand: chain 'H' and resid 390 through 394 Processing sheet with id= AH, first strand: chain 'M' and resid 92 through 95 removed outlier: 6.412A pdb=" N VAL M 138 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ILE M 44 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N PHE M 140 " --> pdb=" O ILE M 44 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'M' and resid 282 through 286 Processing sheet with id= AJ, first strand: chain 'M' and resid 356 through 361 removed outlier: 6.189A pdb=" N ASN M 382 " --> pdb=" O VAL M 357 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE M 359 " --> pdb=" O ASN M 382 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL M 384 " --> pdb=" O ILE M 359 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N ALA M 361 " --> pdb=" O VAL M 384 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL M 386 " --> pdb=" O ALA M 361 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR M 387 " --> pdb=" O ILE M 445 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE M 445 " --> pdb=" O THR M 387 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N SER M 389 " --> pdb=" O ILE M 443 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE M 443 " --> pdb=" O SER M 389 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N PHE M 419 " --> pdb=" O VAL M 412 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N VAL M 412 " --> pdb=" O PHE M 419 " (cutoff:3.500A) 878 hydrogen bonds defined for protein. 2481 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 95 stacking parallelities Total time for adding SS restraints: 11.26 Time building geometry restraints manager: 14.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8567 1.33 - 1.46: 7187 1.46 - 1.58: 16964 1.58 - 1.70: 276 1.70 - 1.82: 148 Bond restraints: 33142 Sorted by residual: bond pdb=" C2' AR6 H 501 " pdb=" C3' AR6 H 501 " ideal model delta sigma weight residual 1.532 1.235 0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C2' AR6 A 501 " pdb=" C3' AR6 A 501 " ideal model delta sigma weight residual 1.532 1.240 0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" C3D AR6 A 501 " pdb=" C4D AR6 A 501 " ideal model delta sigma weight residual 1.529 1.254 0.275 2.00e-02 2.50e+03 1.89e+02 bond pdb=" C3D AR6 H 501 " pdb=" C4D AR6 H 501 " ideal model delta sigma weight residual 1.529 1.259 0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C1D AR6 H 501 " pdb=" C2D AR6 H 501 " ideal model delta sigma weight residual 1.529 1.287 0.242 2.00e-02 2.50e+03 1.46e+02 ... (remaining 33137 not shown) Histogram of bond angle deviations from ideal: 96.65 - 104.22: 897 104.22 - 111.80: 15825 111.80 - 119.38: 11687 119.38 - 126.95: 16238 126.95 - 134.53: 729 Bond angle restraints: 45376 Sorted by residual: angle pdb=" C LEU A 39 " pdb=" N ASP A 40 " pdb=" CA ASP A 40 " ideal model delta sigma weight residual 121.54 133.61 -12.07 1.91e+00 2.74e-01 3.99e+01 angle pdb=" O3A AR6 A 501 " pdb=" PA AR6 A 501 " pdb=" O5' AR6 A 501 " ideal model delta sigma weight residual 93.19 110.39 -17.20 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C LEU F 39 " pdb=" N ASP F 40 " pdb=" CA ASP F 40 " ideal model delta sigma weight residual 121.54 132.26 -10.72 1.91e+00 2.74e-01 3.15e+01 angle pdb=" C GLU M 352 " pdb=" N TYR M 353 " pdb=" CA TYR M 353 " ideal model delta sigma weight residual 120.49 128.24 -7.75 1.42e+00 4.96e-01 2.98e+01 angle pdb=" C ALA H 145 " pdb=" CA ALA H 145 " pdb=" CB ALA H 145 " ideal model delta sigma weight residual 116.63 110.40 6.23 1.16e+00 7.43e-01 2.88e+01 ... (remaining 45371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.52: 18761 32.52 - 65.03: 589 65.03 - 97.55: 45 97.55 - 130.07: 5 130.07 - 162.58: 12 Dihedral angle restraints: 19412 sinusoidal: 8904 harmonic: 10508 Sorted by residual: dihedral pdb=" O4' U N 9 " pdb=" C1' U N 9 " pdb=" N1 U N 9 " pdb=" C2 U N 9 " ideal model delta sinusoidal sigma weight residual 200.00 37.42 162.58 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' U I 9 " pdb=" C1' U I 9 " pdb=" N1 U I 9 " pdb=" C2 U I 9 " ideal model delta sinusoidal sigma weight residual 200.00 40.57 159.43 1 1.50e+01 4.44e-03 8.26e+01 dihedral pdb=" O4' U O 13 " pdb=" C1' U O 13 " pdb=" N1 U O 13 " pdb=" C2 U O 13 " ideal model delta sinusoidal sigma weight residual 200.00 41.01 158.99 1 1.50e+01 4.44e-03 8.25e+01 ... (remaining 19409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4398 0.064 - 0.128: 550 0.128 - 0.192: 28 0.192 - 0.256: 5 0.256 - 0.321: 3 Chirality restraints: 4984 Sorted by residual: chirality pdb=" C3' AR6 H 501 " pdb=" C2' AR6 H 501 " pdb=" C4' AR6 H 501 " pdb=" O3' AR6 H 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.39 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C3' AR6 A 501 " pdb=" C2' AR6 A 501 " pdb=" C4' AR6 A 501 " pdb=" O3' AR6 A 501 " both_signs ideal model delta sigma weight residual False -2.71 -2.40 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE C 7 " pdb=" CA ILE C 7 " pdb=" CG1 ILE C 7 " pdb=" CG2 ILE C 7 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 4981 not shown) Planarity restraints: 5238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 194 " -0.070 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO C 195 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 195 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO C 195 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 143 " -0.048 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO G 144 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO G 144 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 144 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 86 " -0.020 2.00e-02 2.50e+03 1.77e-02 7.80e+00 pdb=" CG TRP M 86 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP M 86 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP M 86 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP M 86 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP M 86 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP M 86 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 86 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 86 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP M 86 " -0.005 2.00e-02 2.50e+03 ... (remaining 5235 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 850 2.67 - 3.23: 31382 3.23 - 3.78: 53111 3.78 - 4.34: 72864 4.34 - 4.90: 112613 Nonbonded interactions: 270820 Sorted by model distance: nonbonded pdb=" OG SER M 493 " pdb=" OD1 ASP M 495 " model vdw 2.112 2.440 nonbonded pdb=" OG SER F 404 " pdb=" OE1 GLU F 406 " model vdw 2.135 2.440 nonbonded pdb=" OG1 THR G 387 " pdb=" OD1 ASN G 446 " model vdw 2.136 2.440 nonbonded pdb=" OH TYR F 416 " pdb=" O THR G 404 " model vdw 2.151 2.440 nonbonded pdb=" OG1 THR G 363 " pdb=" OP1 DA P 8 " model vdw 2.168 2.440 ... (remaining 270815 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 1 through 418) selection = chain 'C' selection = chain 'F' selection = (chain 'H' and resid 1 through 418) } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'M' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.210 Construct map_model_manager: 0.050 Extract box with map and model: 7.700 Check model and map are aligned: 0.480 Set scattering table: 0.300 Process input model: 93.550 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.260 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.297 33142 Z= 0.348 Angle : 0.748 17.195 45376 Z= 0.420 Chirality : 0.042 0.321 4984 Planarity : 0.005 0.104 5238 Dihedral : 15.799 162.584 12620 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.87 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.14), residues: 3532 helix: 0.59 (0.16), residues: 1156 sheet: -0.62 (0.21), residues: 558 loop : -1.29 (0.14), residues: 1818 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 3.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.4073 time to fit residues: 273.8168 Evaluate side-chains 269 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 3.776 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 8.9990 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 93 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 282 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 171 optimal weight: 0.9980 chunk 210 optimal weight: 20.0000 chunk 326 optimal weight: 0.8980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 87 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 18 GLN E 209 GLN ** E 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS F 267 GLN F 270 ASN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 HIS H 69 ASN H 314 GLN ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 222 GLN M 251 HIS ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 33142 Z= 0.319 Angle : 0.687 9.466 45376 Z= 0.357 Chirality : 0.044 0.169 4984 Planarity : 0.006 0.068 5238 Dihedral : 15.436 172.093 5332 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.32 % Favored : 94.34 % Rotamer: Outliers : 1.47 % Allowed : 8.35 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.01 (0.14), residues: 3532 helix: 0.41 (0.15), residues: 1172 sheet: -0.93 (0.20), residues: 596 loop : -1.29 (0.14), residues: 1764 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 298 time to evaluate : 3.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 39 residues processed: 324 average time/residue: 0.3922 time to fit residues: 215.1688 Evaluate side-chains 290 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 251 time to evaluate : 3.855 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.2907 time to fit residues: 26.3224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 90 optimal weight: 10.0000 chunk 327 optimal weight: 9.9990 chunk 353 optimal weight: 3.9990 chunk 291 optimal weight: 9.9990 chunk 324 optimal weight: 7.9990 chunk 111 optimal weight: 4.9990 chunk 262 optimal weight: 0.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 209 GLN ** E 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 409 ASN ** M 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33142 Z= 0.217 Angle : 0.601 12.566 45376 Z= 0.310 Chirality : 0.042 0.162 4984 Planarity : 0.005 0.071 5238 Dihedral : 15.367 170.502 5332 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.37 % Allowed : 4.78 % Favored : 94.85 % Rotamer: Outliers : 0.72 % Allowed : 11.83 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.14), residues: 3532 helix: 0.52 (0.15), residues: 1196 sheet: -0.85 (0.21), residues: 584 loop : -1.24 (0.14), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 304 time to evaluate : 3.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 323 average time/residue: 0.4285 time to fit residues: 227.9266 Evaluate side-chains 265 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 255 time to evaluate : 3.725 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2784 time to fit residues: 10.2041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 chunk 169 optimal weight: 0.6980 chunk 36 optimal weight: 20.0000 chunk 156 optimal weight: 0.5980 chunk 219 optimal weight: 3.9990 chunk 328 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 171 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 446 ASN F 160 HIS F 283 GLN ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 33142 Z= 0.171 Angle : 0.570 10.309 45376 Z= 0.293 Chirality : 0.041 0.168 4984 Planarity : 0.005 0.062 5238 Dihedral : 15.264 170.482 5332 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.98 % Favored : 94.71 % Rotamer: Outliers : 1.16 % Allowed : 12.86 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.14), residues: 3532 helix: 0.69 (0.15), residues: 1198 sheet: -0.68 (0.21), residues: 604 loop : -1.16 (0.14), residues: 1730 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 285 time to evaluate : 3.892 Fit side-chains 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: 18 residues processed: 310 average time/residue: 0.4179 time to fit residues: 216.9771 Evaluate side-chains 275 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 257 time to evaluate : 3.650 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2889 time to fit residues: 14.9034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 296 optimal weight: 20.0000 chunk 240 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 312 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 overall best weight: 4.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 HIS ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 358 HIS ** F 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 314 GLN ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 59 HIS M 251 HIS ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 468 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 33142 Z= 0.346 Angle : 0.721 12.237 45376 Z= 0.375 Chirality : 0.045 0.211 4984 Planarity : 0.006 0.064 5238 Dihedral : 15.634 168.730 5332 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 24.99 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.51 % Favored : 93.12 % Rotamer: Outliers : 1.69 % Allowed : 15.08 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % 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: -1.22 (0.14), residues: 3532 helix: 0.11 (0.15), residues: 1202 sheet: -1.18 (0.21), residues: 590 loop : -1.29 (0.14), residues: 1740 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 266 time to evaluate : 3.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 33 residues processed: 307 average time/residue: 0.4184 time to fit residues: 215.4056 Evaluate side-chains 269 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 236 time to evaluate : 3.736 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.3054 time to fit residues: 24.1862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 6.9990 chunk 313 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 204 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 348 optimal weight: 0.6980 chunk 289 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 28 optimal weight: 40.0000 chunk 115 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 327 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 HIS F 364 GLN G 59 HIS ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 33142 Z= 0.229 Angle : 0.610 8.963 45376 Z= 0.314 Chirality : 0.042 0.164 4984 Planarity : 0.005 0.061 5238 Dihedral : 15.501 172.366 5332 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 18.53 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.27 % Favored : 94.39 % Rotamer: Outliers : 1.03 % Allowed : 16.33 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3532 helix: 0.36 (0.15), residues: 1218 sheet: -1.10 (0.21), residues: 600 loop : -1.18 (0.15), residues: 1714 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 278 time to evaluate : 3.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 16 residues processed: 300 average time/residue: 0.4180 time to fit residues: 209.5433 Evaluate side-chains 262 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 246 time to evaluate : 3.643 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.2878 time to fit residues: 13.6499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 9.9990 chunk 39 optimal weight: 20.0000 chunk 198 optimal weight: 8.9990 chunk 254 optimal weight: 8.9990 chunk 197 optimal weight: 8.9990 chunk 293 optimal weight: 20.0000 chunk 194 optimal weight: 0.7980 chunk 346 optimal weight: 9.9990 chunk 217 optimal weight: 8.9990 chunk 211 optimal weight: 20.0000 chunk 160 optimal weight: 9.9990 overall best weight: 7.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 61 GLN ** E 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 HIS ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 360 HIS G 439 ASN ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS ** M 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 33142 Z= 0.491 Angle : 0.820 11.830 45376 Z= 0.429 Chirality : 0.049 0.284 4984 Planarity : 0.006 0.079 5238 Dihedral : 16.046 170.790 5332 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 29.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.53 % Favored : 92.10 % Rotamer: Outliers : 1.28 % Allowed : 17.68 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3532 helix: -0.37 (0.14), residues: 1198 sheet: -1.88 (0.20), residues: 608 loop : -1.38 (0.15), residues: 1726 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 240 time to evaluate : 3.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 29 residues processed: 272 average time/residue: 0.4324 time to fit residues: 198.7789 Evaluate side-chains 253 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 3.758 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.2822 time to fit residues: 20.9416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 207 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 220 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 171 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 272 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 405 ASN G 59 HIS ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 ASN ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS ** M 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33142 Z= 0.296 Angle : 0.675 9.769 45376 Z= 0.349 Chirality : 0.044 0.248 4984 Planarity : 0.005 0.072 5238 Dihedral : 15.832 173.445 5332 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.34 % Favored : 93.29 % Rotamer: Outliers : 0.47 % Allowed : 18.68 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.14 % 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 (0.14), residues: 3532 helix: -0.05 (0.15), residues: 1212 sheet: -1.71 (0.20), residues: 628 loop : -1.32 (0.15), residues: 1692 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 257 time to evaluate : 3.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 265 average time/residue: 0.4413 time to fit residues: 196.7513 Evaluate side-chains 244 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 235 time to evaluate : 3.732 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2941 time to fit residues: 10.0416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 1.9990 chunk 332 optimal weight: 1.9990 chunk 303 optimal weight: 10.0000 chunk 323 optimal weight: 4.9990 chunk 194 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 253 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 305 optimal weight: 10.0000 chunk 322 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS ** M 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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 : 0.004 0.046 33142 Z= 0.273 Angle : 0.672 13.343 45376 Z= 0.344 Chirality : 0.044 0.311 4984 Planarity : 0.005 0.065 5238 Dihedral : 15.781 175.112 5332 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.82 % Favored : 92.81 % Rotamer: Outliers : 0.31 % Allowed : 19.43 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % 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: -1.39 (0.14), residues: 3532 helix: 0.12 (0.15), residues: 1200 sheet: -1.66 (0.20), residues: 628 loop : -1.32 (0.15), residues: 1704 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 252 time to evaluate : 3.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 257 average time/residue: 0.4227 time to fit residues: 184.9728 Evaluate side-chains 235 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 231 time to evaluate : 3.858 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2721 time to fit residues: 6.8874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 5.9990 chunk 341 optimal weight: 9.9990 chunk 208 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 237 optimal weight: 0.0170 chunk 358 optimal weight: 10.0000 chunk 330 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 175 optimal weight: 0.0010 overall best weight: 3.6030 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 ASN ** F 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 293 ASN ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS ** M 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.5145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33142 Z= 0.281 Angle : 0.678 11.188 45376 Z= 0.347 Chirality : 0.044 0.307 4984 Planarity : 0.005 0.070 5238 Dihedral : 15.791 175.746 5332 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.16 % Favored : 92.55 % Rotamer: Outliers : 0.41 % Allowed : 19.84 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.43 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3532 helix: 0.13 (0.15), residues: 1200 sheet: -1.68 (0.20), residues: 628 loop : -1.34 (0.15), residues: 1704 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7064 Ramachandran restraints generated. 3532 Oldfield, 0 Emsley, 3532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 241 time to evaluate : 3.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 247 average time/residue: 0.4344 time to fit residues: 180.4919 Evaluate side-chains 240 residues out of total 3196 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 232 time to evaluate : 3.628 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.2992 time to fit residues: 9.3404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 0.9990 chunk 304 optimal weight: 30.0000 chunk 87 optimal weight: 6.9990 chunk 263 optimal weight: 0.0010 chunk 42 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 286 optimal weight: 10.0000 chunk 119 optimal weight: 9.9990 chunk 293 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 409 ASN ** B 446 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS ** M 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.093347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.074202 restraints weight = 154713.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.075899 restraints weight = 93718.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.077024 restraints weight = 68411.900| |-----------------------------------------------------------------------------| r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 33142 Z= 0.210 Angle : 0.650 12.595 45376 Z= 0.327 Chirality : 0.043 0.382 4984 Planarity : 0.005 0.073 5238 Dihedral : 15.623 177.878 5332 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.31 % Favored : 93.43 % Rotamer: Outliers : 0.09 % Allowed : 20.24 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.71 % 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: -1.22 (0.14), residues: 3532 helix: 0.37 (0.15), residues: 1198 sheet: -1.60 (0.20), residues: 664 loop : -1.28 (0.15), residues: 1670 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5686.94 seconds wall clock time: 106 minutes 46.86 seconds (6406.86 seconds total)