Starting phenix.real_space_refine on Tue Apr 9 05:08:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/04_2024/8op1_17035.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/04_2024/8op1_17035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/04_2024/8op1_17035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/04_2024/8op1_17035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/04_2024/8op1_17035.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op1_17035/04_2024/8op1_17035.pdb" } resolution = 3.5 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 35 5.49 5 S 80 5.16 5 C 9630 2.51 5 N 2655 2.21 5 O 3015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "A TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 369": "OD1" <-> "OD2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "B ASP 10": "OD1" <-> "OD2" Residue "B TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 141": "OE1" <-> "OE2" Residue "B ASP 345": "OD1" <-> "OD2" Residue "B GLU 373": "OE1" <-> "OE2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C GLU 214": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C GLU 355": "OE1" <-> "OE2" Residue "C ASP 369": "OD1" <-> "OD2" Residue "C GLU 373": "OE1" <-> "OE2" Residue "D GLU 55": "OE1" <-> "OE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "D TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 376": "OE1" <-> "OE2" Residue "E GLU 55": "OE1" <-> "OE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 85": "OD1" <-> "OD2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 204": "OD1" <-> "OD2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 374": "OE1" <-> "OE2" Residue "E GLU 376": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15415 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "B" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "C" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "H" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "D" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "I" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "E" Number of atoms: 2943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2943 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 8, 'TRANS': 369} Chain: "J" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Time building chain proxies: 8.41, per 1000 atoms: 0.55 Number of scatterers: 15415 At special positions: 0 Unit cell: (178.62, 117.935, 117.935, 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 80 16.00 P 35 15.00 O 3015 8.00 N 2655 7.00 C 9630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.96 Conformation dependent library (CDL) restraints added in 2.6 seconds 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3470 Finding SS restraints... Secondary structure from input PDB file: 110 helices and 13 sheets defined 68.0% alpha, 4.8% beta 0 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 4.80 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 54 Processing helix chain 'A' and resid 58 through 61 removed outlier: 4.168A pdb=" N PHE A 61 " --> pdb=" O ASN A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 62 through 75 Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 121 through 143 Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.563A pdb=" N ARG A 150 " --> pdb=" O PRO A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 171 Processing helix chain 'A' and resid 178 through 189 Processing helix chain 'A' and resid 190 through 197 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.097A pdb=" N ASP A 221 " --> pdb=" O PRO A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 248 Processing helix chain 'A' and resid 255 through 267 removed outlier: 3.764A pdb=" N ARG A 259 " --> pdb=" O GLN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 274 through 279 Processing helix chain 'A' and resid 280 through 295 Processing helix chain 'A' and resid 296 through 300 removed outlier: 3.825A pdb=" N GLY A 299 " --> pdb=" O GLY A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 3.755A pdb=" N SER A 310 " --> pdb=" O PRO A 307 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 311 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 313 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 Processing helix chain 'A' and resid 343 through 360 removed outlier: 3.806A pdb=" N GLU A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASN A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.529A pdb=" N VAL B 6 " --> pdb=" O LEU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 20 Processing helix chain 'B' and resid 40 through 54 Processing helix chain 'B' and resid 58 through 60 No H-bonds generated for 'chain 'B' and resid 58 through 60' Processing helix chain 'B' and resid 61 through 75 removed outlier: 4.044A pdb=" N ILE B 65 " --> pdb=" O PHE B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 120 through 143 removed outlier: 3.535A pdb=" N GLN B 124 " --> pdb=" O THR B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 150 removed outlier: 3.645A pdb=" N ARG B 150 " --> pdb=" O PRO B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 170 Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 178 through 189 Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 201 through 216 Processing helix chain 'B' and resid 216 through 231 removed outlier: 4.175A pdb=" N ILE B 220 " --> pdb=" O HIS B 216 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASP B 221 " --> pdb=" O PRO B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 251 removed outlier: 3.622A pdb=" N ASN B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR B 251 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 removed outlier: 4.173A pdb=" N ARG B 259 " --> pdb=" O GLN B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 273 removed outlier: 3.553A pdb=" N LEU B 272 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 279 Processing helix chain 'B' and resid 280 through 295 Processing helix chain 'B' and resid 296 through 300 removed outlier: 4.094A pdb=" N GLY B 299 " --> pdb=" O GLY B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 4.010A pdb=" N SER B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 311 " --> pdb=" O LYS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 331 Processing helix chain 'B' and resid 343 through 360 removed outlier: 3.630A pdb=" N GLU B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 379 removed outlier: 4.143A pdb=" N ALA B 377 " --> pdb=" O GLU B 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 54 removed outlier: 3.523A pdb=" N THR C 54 " --> pdb=" O MET C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 60 No H-bonds generated for 'chain 'C' and resid 58 through 60' Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.604A pdb=" N GLN C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 171 Processing helix chain 'C' and resid 178 through 189 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 201 through 216 Processing helix chain 'C' and resid 216 through 231 removed outlier: 4.076A pdb=" N ILE C 220 " --> pdb=" O HIS C 216 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP C 221 " --> pdb=" O PRO C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 248 Processing helix chain 'C' and resid 255 through 267 removed outlier: 3.727A pdb=" N ARG C 259 " --> pdb=" O GLN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 274 through 295 removed outlier: 4.006A pdb=" N GLU C 280 " --> pdb=" O SER C 276 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLU C 282 " --> pdb=" O GLN C 278 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLN C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 298 No H-bonds generated for 'chain 'C' and resid 296 through 298' Processing helix chain 'C' and resid 309 through 313 Processing helix chain 'C' and resid 317 through 331 Processing helix chain 'C' and resid 343 through 360 removed outlier: 4.101A pdb=" N GLU C 359 " --> pdb=" O GLU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 379 Processing helix chain 'D' and resid 10 through 20 Processing helix chain 'D' and resid 40 through 54 Processing helix chain 'D' and resid 58 through 60 No H-bonds generated for 'chain 'D' and resid 58 through 60' Processing helix chain 'D' and resid 61 through 75 removed outlier: 3.903A pdb=" N ILE D 65 " --> pdb=" O PHE D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 87 Processing helix chain 'D' and resid 120 through 143 Processing helix chain 'D' and resid 146 through 150 removed outlier: 3.584A pdb=" N ARG D 150 " --> pdb=" O PRO D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 170 Processing helix chain 'D' and resid 178 through 189 Processing helix chain 'D' and resid 190 through 197 Processing helix chain 'D' and resid 201 through 216 Processing helix chain 'D' and resid 217 through 231 removed outlier: 3.884A pdb=" N ASP D 221 " --> pdb=" O PRO D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 248 Processing helix chain 'D' and resid 255 through 267 removed outlier: 3.926A pdb=" N ARG D 259 " --> pdb=" O GLN D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 273 removed outlier: 3.634A pdb=" N LEU D 272 " --> pdb=" O ASN D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 279 Processing helix chain 'D' and resid 280 through 295 Processing helix chain 'D' and resid 296 through 300 removed outlier: 4.150A pdb=" N GLY D 299 " --> pdb=" O GLY D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 4.341A pdb=" N SER D 310 " --> pdb=" O PRO D 307 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU D 311 " --> pdb=" O LYS D 308 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 313 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 331 Processing helix chain 'D' and resid 343 through 360 removed outlier: 3.611A pdb=" N GLU D 359 " --> pdb=" O GLU D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 379 Processing helix chain 'E' and resid 10 through 20 Processing helix chain 'E' and resid 40 through 54 Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 76 through 86 Processing helix chain 'E' and resid 120 through 143 removed outlier: 3.825A pdb=" N GLN E 124 " --> pdb=" O THR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 150 removed outlier: 3.725A pdb=" N ARG E 150 " --> pdb=" O PRO E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 171 Processing helix chain 'E' and resid 178 through 189 Processing helix chain 'E' and resid 190 through 197 Processing helix chain 'E' and resid 201 through 216 Processing helix chain 'E' and resid 217 through 231 removed outlier: 4.316A pdb=" N ASP E 221 " --> pdb=" O PRO E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 248 Processing helix chain 'E' and resid 255 through 267 removed outlier: 3.909A pdb=" N ARG E 259 " --> pdb=" O GLN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 273 removed outlier: 3.572A pdb=" N LEU E 272 " --> pdb=" O ASN E 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 279 Processing helix chain 'E' and resid 280 through 295 Processing helix chain 'E' and resid 296 through 299 removed outlier: 3.786A pdb=" N GLY E 299 " --> pdb=" O GLY E 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 296 through 299' Processing helix chain 'E' and resid 306 through 313 removed outlier: 4.159A pdb=" N SER E 310 " --> pdb=" O PRO E 307 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU E 311 " --> pdb=" O LYS E 308 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER E 313 " --> pdb=" O SER E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 331 Processing helix chain 'E' and resid 343 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 28 removed outlier: 7.222A pdb=" N ARG A 27 " --> pdb=" O HIS A 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.626A pdb=" N ILE A 33 " --> pdb=" O ASN A 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 104 removed outlier: 3.648A pdb=" N PHE A 111 " --> pdb=" O HIS A 100 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 102 " --> pdb=" O MET A 109 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 109 " --> pdb=" O GLN A 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 28 removed outlier: 7.071A pdb=" N ARG B 27 " --> pdb=" O HIS B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 33 through 34 removed outlier: 6.972A pdb=" N ILE B 33 " --> pdb=" O ASN B 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 104 removed outlier: 4.200A pdb=" N ASP B 96 " --> pdb=" O THR B 115 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 27 through 28 removed outlier: 7.165A pdb=" N ARG C 27 " --> pdb=" O HIS C 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 35 removed outlier: 3.599A pdb=" N ASN C 93 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 97 through 104 removed outlier: 3.532A pdb=" N GLN C 102 " --> pdb=" O MET C 109 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET C 109 " --> pdb=" O GLN C 102 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 33 through 34 removed outlier: 6.554A pdb=" N ILE D 33 " --> pdb=" O ASN D 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 97 through 104 removed outlier: 3.747A pdb=" N HIS D 100 " --> pdb=" O PHE D 111 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N PHE D 111 " --> pdb=" O HIS D 100 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 33 through 34 removed outlier: 6.438A pdb=" N ILE E 33 " --> pdb=" O ASN E 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'E' and resid 97 through 104 removed outlier: 3.525A pdb=" N PHE E 111 " --> pdb=" O HIS E 100 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN E 102 " --> pdb=" O MET E 109 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET E 109 " --> pdb=" O GLN E 102 " (cutoff:3.500A) 851 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 4.81 Time building geometry restraints manager: 6.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5025 1.34 - 1.46: 3297 1.46 - 1.58: 7188 1.58 - 1.70: 65 1.70 - 1.82: 145 Bond restraints: 15720 Sorted by residual: bond pdb=" C ILE C 270 " pdb=" N MET C 271 " ideal model delta sigma weight residual 1.335 1.305 0.030 1.39e-02 5.18e+03 4.55e+00 bond pdb=" CA MET C 271 " pdb=" C MET C 271 " ideal model delta sigma weight residual 1.524 1.493 0.030 1.59e-02 3.96e+03 3.61e+00 bond pdb=" CA SER A 231 " pdb=" C SER A 231 " ideal model delta sigma weight residual 1.522 1.494 0.027 1.72e-02 3.38e+03 2.51e+00 bond pdb=" N LYS A 7 " pdb=" CA LYS A 7 " ideal model delta sigma weight residual 1.464 1.444 0.019 1.25e-02 6.40e+03 2.39e+00 bond pdb=" CA MET B 271 " pdb=" C MET B 271 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.80e-02 3.09e+03 2.12e+00 ... (remaining 15715 not shown) Histogram of bond angle deviations from ideal: 96.90 - 104.32: 281 104.32 - 111.73: 7373 111.73 - 119.15: 5553 119.15 - 126.56: 7996 126.56 - 133.97: 112 Bond angle restraints: 21315 Sorted by residual: angle pdb=" C GLU C 55 " pdb=" N ASP C 56 " pdb=" CA ASP C 56 " ideal model delta sigma weight residual 121.54 128.38 -6.84 1.91e+00 2.74e-01 1.28e+01 angle pdb=" N VAL D 267 " pdb=" CA VAL D 267 " pdb=" C VAL D 267 " ideal model delta sigma weight residual 112.98 108.60 4.38 1.25e+00 6.40e-01 1.23e+01 angle pdb=" N ILE E 378 " pdb=" CA ILE E 378 " pdb=" C ILE E 378 " ideal model delta sigma weight residual 113.42 109.41 4.01 1.17e+00 7.31e-01 1.18e+01 angle pdb=" N VAL C 267 " pdb=" CA VAL C 267 " pdb=" C VAL C 267 " ideal model delta sigma weight residual 113.07 108.63 4.44 1.36e+00 5.41e-01 1.06e+01 angle pdb=" N GLY C 296 " pdb=" CA GLY C 296 " pdb=" C GLY C 296 " ideal model delta sigma weight residual 112.50 116.23 -3.73 1.16e+00 7.43e-01 1.03e+01 ... (remaining 21310 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 8507 17.60 - 35.19: 855 35.19 - 52.79: 156 52.79 - 70.39: 29 70.39 - 87.98: 53 Dihedral angle restraints: 9600 sinusoidal: 4165 harmonic: 5435 Sorted by residual: dihedral pdb=" CA ILE A 303 " pdb=" C ILE A 303 " pdb=" N LEU A 304 " pdb=" CA LEU A 304 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA ILE B 303 " pdb=" C ILE B 303 " pdb=" N LEU B 304 " pdb=" CA LEU B 304 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ILE C 303 " pdb=" C ILE C 303 " pdb=" N LEU C 304 " pdb=" CA LEU C 304 " ideal model delta harmonic sigma weight residual 180.00 154.58 25.42 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 9597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1811 0.049 - 0.098: 539 0.098 - 0.147: 92 0.147 - 0.196: 7 0.196 - 0.245: 1 Chirality restraints: 2450 Sorted by residual: chirality pdb=" CB THR C 35 " pdb=" CA THR C 35 " pdb=" OG1 THR C 35 " pdb=" CG2 THR C 35 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.25 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CA MET B 142 " pdb=" N MET B 142 " pdb=" C MET B 142 " pdb=" CB MET B 142 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.20e-01 chirality pdb=" CA MET C 271 " pdb=" N MET C 271 " pdb=" C MET C 271 " pdb=" CB MET C 271 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.17 2.00e-01 2.50e+01 6.84e-01 ... (remaining 2447 not shown) Planarity restraints: 2620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 306 " 0.055 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO C 307 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 216 " 0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO A 217 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 306 " -0.034 5.00e-02 4.00e+02 5.04e-02 4.07e+00 pdb=" N PRO B 307 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 307 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 307 " -0.028 5.00e-02 4.00e+02 ... (remaining 2617 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 514 2.70 - 3.25: 16106 3.25 - 3.80: 24655 3.80 - 4.35: 31316 4.35 - 4.90: 52085 Nonbonded interactions: 124676 Sorted by model distance: nonbonded pdb=" OH TYR B 69 " pdb=" NH2 ARG B 73 " model vdw 2.154 2.520 nonbonded pdb=" OH TYR D 337 " pdb=" OP2 C I1004 " model vdw 2.160 2.440 nonbonded pdb=" O ASP B 31 " pdb=" NZ LYS B 91 " model vdw 2.162 2.520 nonbonded pdb=" OG SER E 32 " pdb=" O LYS E 91 " model vdw 2.163 2.440 nonbonded pdb=" OH TYR E 135 " pdb=" NH1 ARG E 150 " model vdw 2.184 2.520 ... (remaining 124671 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.100 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 44.680 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 0.062 15720 Z= 0.400 Angle : 0.747 9.217 21315 Z= 0.420 Chirality : 0.046 0.245 2450 Planarity : 0.004 0.081 2620 Dihedral : 15.507 87.981 6130 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.19), residues: 1880 helix: 0.18 (0.15), residues: 1138 sheet: 1.49 (0.56), residues: 76 loop : -1.09 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 260 HIS 0.010 0.002 HIS E 216 PHE 0.014 0.002 PHE A 226 TYR 0.031 0.002 TYR D 301 ARG 0.008 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 1.731 Fit side-chains REVERT: A 50 MET cc_start: 0.8339 (mpp) cc_final: 0.8074 (mpp) REVERT: B 12 LEU cc_start: 0.8915 (tp) cc_final: 0.8483 (tp) REVERT: B 50 MET cc_start: 0.6837 (mpp) cc_final: 0.6388 (mpp) REVERT: C 67 MET cc_start: 0.8532 (mmm) cc_final: 0.7725 (mmt) REVERT: D 138 MET cc_start: 0.7424 (mtp) cc_final: 0.6628 (tmm) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2491 time to fit residues: 71.1139 Evaluate side-chains 146 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.3980 chunk 140 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 74 optimal weight: 0.7980 chunk 145 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 GLN ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS C 151 HIS C 249 ASN ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15720 Z= 0.203 Angle : 0.541 6.689 21315 Z= 0.286 Chirality : 0.041 0.187 2450 Planarity : 0.003 0.042 2620 Dihedral : 11.170 73.689 2590 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.76 % Allowed : 8.25 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.19), residues: 1880 helix: 0.80 (0.15), residues: 1156 sheet: 2.02 (0.63), residues: 68 loop : -1.02 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 260 HIS 0.006 0.001 HIS E 216 PHE 0.014 0.001 PHE E 219 TYR 0.015 0.001 TYR A 210 ARG 0.005 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 175 time to evaluate : 1.574 Fit side-chains REVERT: A 50 MET cc_start: 0.8244 (mpp) cc_final: 0.7981 (mpp) REVERT: B 50 MET cc_start: 0.6855 (mpp) cc_final: 0.6496 (mpp) REVERT: C 67 MET cc_start: 0.8647 (mmm) cc_final: 0.7974 (mmt) REVERT: C 80 ILE cc_start: 0.6867 (mm) cc_final: 0.6551 (tp) REVERT: C 257 MET cc_start: 0.8263 (mmm) cc_final: 0.7943 (mmt) REVERT: D 138 MET cc_start: 0.7597 (mtp) cc_final: 0.6589 (tmm) outliers start: 12 outliers final: 9 residues processed: 182 average time/residue: 0.2529 time to fit residues: 71.8038 Evaluate side-chains 162 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 153 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 151 HIS Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain E residue 201 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 139 optimal weight: 0.9980 chunk 114 optimal weight: 0.0870 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 181 optimal weight: 0.0570 chunk 149 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 43 HIS ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 45 ASN C 89 HIS ** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 15720 Z= 0.167 Angle : 0.503 7.701 21315 Z= 0.264 Chirality : 0.040 0.182 2450 Planarity : 0.003 0.031 2620 Dihedral : 11.091 73.681 2590 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.46 % Allowed : 10.98 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1880 helix: 1.05 (0.15), residues: 1163 sheet: 2.67 (0.63), residues: 62 loop : -0.95 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 260 HIS 0.011 0.001 HIS C 151 PHE 0.011 0.001 PHE D 226 TYR 0.012 0.001 TYR C 337 ARG 0.005 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: A 50 MET cc_start: 0.8260 (mpp) cc_final: 0.8054 (mpp) REVERT: B 50 MET cc_start: 0.6672 (mpp) cc_final: 0.6422 (mtt) REVERT: B 158 MET cc_start: 0.7959 (mmt) cc_final: 0.7503 (mmt) REVERT: B 256 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7851 (m) REVERT: C 80 ILE cc_start: 0.6889 (mm) cc_final: 0.6544 (tp) REVERT: D 27 ARG cc_start: 0.2874 (OUTLIER) cc_final: 0.1816 (mmp-170) REVERT: D 138 MET cc_start: 0.7667 (mtp) cc_final: 0.6537 (tmm) outliers start: 23 outliers final: 16 residues processed: 188 average time/residue: 0.2561 time to fit residues: 74.4019 Evaluate side-chains 170 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 152 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 0.1980 chunk 126 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 0.5980 chunk 168 optimal weight: 0.9980 chunk 178 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 160 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS C 249 ASN ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15720 Z= 0.201 Angle : 0.516 8.448 21315 Z= 0.268 Chirality : 0.040 0.149 2450 Planarity : 0.003 0.031 2620 Dihedral : 11.033 73.694 2590 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.35 % Allowed : 12.89 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 1880 helix: 1.12 (0.15), residues: 1163 sheet: 2.68 (0.62), residues: 62 loop : -0.90 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 260 HIS 0.005 0.001 HIS C 89 PHE 0.011 0.001 PHE D 226 TYR 0.021 0.001 TYR C 337 ARG 0.004 0.000 ARG C 73 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 161 time to evaluate : 1.716 Fit side-chains REVERT: B 50 MET cc_start: 0.6739 (mpp) cc_final: 0.6478 (mtt) REVERT: B 248 MET cc_start: 0.7059 (mmm) cc_final: 0.6812 (mtp) REVERT: B 256 VAL cc_start: 0.8175 (OUTLIER) cc_final: 0.7959 (m) REVERT: C 80 ILE cc_start: 0.6917 (mm) cc_final: 0.6569 (tp) REVERT: C 201 LEU cc_start: 0.6733 (mp) cc_final: 0.6529 (tp) REVERT: D 27 ARG cc_start: 0.2919 (OUTLIER) cc_final: 0.1870 (mmp-170) REVERT: D 138 MET cc_start: 0.7772 (mtp) cc_final: 0.6629 (tmm) outliers start: 37 outliers final: 26 residues processed: 180 average time/residue: 0.2609 time to fit residues: 71.6620 Evaluate side-chains 178 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 2 optimal weight: 0.0370 chunk 133 optimal weight: 0.5980 chunk 73 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 0.0060 chunk 160 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN C 26 GLN C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 15720 Z= 0.152 Angle : 0.485 8.782 21315 Z= 0.251 Chirality : 0.038 0.146 2450 Planarity : 0.003 0.029 2620 Dihedral : 11.030 73.637 2590 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.86 % Allowed : 12.63 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1880 helix: 1.34 (0.15), residues: 1173 sheet: 2.62 (0.61), residues: 62 loop : -0.89 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 260 HIS 0.004 0.001 HIS E 43 PHE 0.009 0.001 PHE D 226 TYR 0.016 0.001 TYR C 337 ARG 0.003 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 163 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7865 (mpt) REVERT: B 50 MET cc_start: 0.6683 (mpp) cc_final: 0.6456 (mtt) REVERT: B 158 MET cc_start: 0.7858 (mmt) cc_final: 0.7539 (mmt) REVERT: B 175 ASP cc_start: 0.7003 (m-30) cc_final: 0.6418 (t0) REVERT: B 256 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7789 (m) REVERT: C 80 ILE cc_start: 0.6992 (mm) cc_final: 0.6636 (tp) REVERT: C 257 MET cc_start: 0.8203 (mmm) cc_final: 0.7845 (mmt) REVERT: D 27 ARG cc_start: 0.3080 (OUTLIER) cc_final: 0.1676 (mmp-170) REVERT: D 138 MET cc_start: 0.7678 (mtp) cc_final: 0.6890 (tmm) outliers start: 45 outliers final: 29 residues processed: 191 average time/residue: 0.2554 time to fit residues: 75.3953 Evaluate side-chains 183 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 151 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 8.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15720 Z= 0.240 Angle : 0.542 11.409 21315 Z= 0.276 Chirality : 0.040 0.155 2450 Planarity : 0.003 0.032 2620 Dihedral : 10.985 73.667 2590 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.60 % Allowed : 13.40 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1880 helix: 1.25 (0.15), residues: 1163 sheet: 2.63 (0.61), residues: 62 loop : -0.80 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 260 HIS 0.006 0.001 HIS E 43 PHE 0.013 0.001 PHE A 226 TYR 0.017 0.001 TYR C 337 ARG 0.003 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 156 time to evaluate : 1.650 Fit side-chains revert: symmetry clash REVERT: A 83 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7323 (mm) REVERT: B 88 TYR cc_start: 0.8077 (m-80) cc_final: 0.7538 (m-80) REVERT: B 175 ASP cc_start: 0.7066 (m-30) cc_final: 0.6650 (t0) REVERT: C 80 ILE cc_start: 0.6963 (mm) cc_final: 0.6476 (tp) REVERT: C 257 MET cc_start: 0.8234 (mmm) cc_final: 0.7886 (mmt) REVERT: C 271 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7444 (mtm) REVERT: D 27 ARG cc_start: 0.3354 (OUTLIER) cc_final: 0.1924 (mmp-170) REVERT: D 138 MET cc_start: 0.7528 (mtp) cc_final: 0.6718 (tmm) REVERT: E 198 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7757 (mtmt) REVERT: E 304 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7436 (mt) outliers start: 41 outliers final: 28 residues processed: 183 average time/residue: 0.2816 time to fit residues: 80.6297 Evaluate side-chains 184 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 151 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain C residue 334 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 198 LYS Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 357 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 178 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 108 optimal weight: 0.0050 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 HIS ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15720 Z= 0.187 Angle : 0.525 11.181 21315 Z= 0.264 Chirality : 0.039 0.149 2450 Planarity : 0.003 0.030 2620 Dihedral : 10.971 73.637 2590 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.41 % Allowed : 14.22 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.20), residues: 1880 helix: 1.32 (0.15), residues: 1172 sheet: 1.93 (0.62), residues: 68 loop : -0.78 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 260 HIS 0.005 0.001 HIS E 43 PHE 0.010 0.001 PHE B 61 TYR 0.017 0.001 TYR C 337 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 1.730 Fit side-chains revert: symmetry clash REVERT: B 88 TYR cc_start: 0.7973 (m-80) cc_final: 0.7431 (m-80) REVERT: B 175 ASP cc_start: 0.7022 (m-30) cc_final: 0.6641 (t0) REVERT: C 80 ILE cc_start: 0.6931 (mm) cc_final: 0.6475 (tp) REVERT: C 257 MET cc_start: 0.8227 (mmm) cc_final: 0.7910 (mmt) REVERT: C 271 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7411 (mtm) REVERT: D 27 ARG cc_start: 0.3397 (OUTLIER) cc_final: 0.1997 (mmp-170) REVERT: D 138 MET cc_start: 0.7646 (mtp) cc_final: 0.6918 (tmm) outliers start: 38 outliers final: 29 residues processed: 181 average time/residue: 0.2515 time to fit residues: 70.3119 Evaluate side-chains 180 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 301 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 113 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 0.8980 chunk 162 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15720 Z= 0.186 Angle : 0.529 16.389 21315 Z= 0.265 Chirality : 0.039 0.164 2450 Planarity : 0.003 0.029 2620 Dihedral : 10.964 73.647 2590 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.48 % Allowed : 14.67 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.97 (0.20), residues: 1880 helix: 1.33 (0.15), residues: 1172 sheet: 1.91 (0.62), residues: 68 loop : -0.75 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 260 HIS 0.004 0.001 HIS C 225 PHE 0.010 0.001 PHE D 226 TYR 0.014 0.001 TYR C 337 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 158 time to evaluate : 1.756 Fit side-chains REVERT: B 88 TYR cc_start: 0.7947 (m-80) cc_final: 0.7662 (m-80) REVERT: B 175 ASP cc_start: 0.6904 (m-30) cc_final: 0.6532 (t0) REVERT: C 80 ILE cc_start: 0.7055 (mm) cc_final: 0.6594 (tp) REVERT: C 257 MET cc_start: 0.8211 (mmm) cc_final: 0.7908 (mmt) REVERT: C 271 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.7331 (mtm) REVERT: D 27 ARG cc_start: 0.3670 (OUTLIER) cc_final: 0.3269 (mtt-85) REVERT: D 138 MET cc_start: 0.7536 (mtp) cc_final: 0.6910 (tmm) REVERT: E 304 LEU cc_start: 0.7779 (OUTLIER) cc_final: 0.7535 (mt) outliers start: 39 outliers final: 31 residues processed: 185 average time/residue: 0.2517 time to fit residues: 72.2723 Evaluate side-chains 185 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 304 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 chunk 109 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15720 Z= 0.218 Angle : 0.561 13.993 21315 Z= 0.279 Chirality : 0.039 0.155 2450 Planarity : 0.003 0.029 2620 Dihedral : 10.958 73.655 2590 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.41 % Allowed : 14.98 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1880 helix: 1.26 (0.15), residues: 1172 sheet: 1.90 (0.61), residues: 68 loop : -0.77 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 260 HIS 0.004 0.001 HIS C 225 PHE 0.010 0.001 PHE B 61 TYR 0.014 0.001 TYR C 337 ARG 0.004 0.000 ARG B 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 154 time to evaluate : 1.854 Fit side-chains REVERT: B 175 ASP cc_start: 0.6970 (m-30) cc_final: 0.6595 (t0) REVERT: C 80 ILE cc_start: 0.7060 (mm) cc_final: 0.6653 (tp) REVERT: C 257 MET cc_start: 0.8246 (mmm) cc_final: 0.7953 (mmt) REVERT: C 271 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7358 (mtm) REVERT: D 27 ARG cc_start: 0.3811 (OUTLIER) cc_final: 0.3099 (mtt90) REVERT: E 304 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7505 (mt) outliers start: 38 outliers final: 33 residues processed: 181 average time/residue: 0.2465 time to fit residues: 69.9967 Evaluate side-chains 188 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 152 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 359 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 323 VAL Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 270 ILE Chi-restraints excluded: chain E residue 301 TYR Chi-restraints excluded: chain E residue 304 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.0570 chunk 107 optimal weight: 0.0270 chunk 83 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 0.0770 chunk 169 optimal weight: 0.7980 chunk 146 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 116 optimal weight: 0.0060 overall best weight: 0.1730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15720 Z= 0.123 Angle : 0.515 11.834 21315 Z= 0.256 Chirality : 0.038 0.158 2450 Planarity : 0.003 0.030 2620 Dihedral : 11.000 73.569 2590 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.78 % Allowed : 16.00 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.20), residues: 1880 helix: 1.49 (0.15), residues: 1173 sheet: 1.88 (0.61), residues: 68 loop : -0.66 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 260 HIS 0.013 0.001 HIS C 89 PHE 0.011 0.001 PHE B 61 TYR 0.015 0.001 TYR C 88 ARG 0.004 0.000 ARG B 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3760 Ramachandran restraints generated. 1880 Oldfield, 0 Emsley, 1880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: B 175 ASP cc_start: 0.7029 (m-30) cc_final: 0.6463 (t0) REVERT: B 257 MET cc_start: 0.8133 (mmt) cc_final: 0.7862 (mmt) REVERT: C 80 ILE cc_start: 0.6984 (mm) cc_final: 0.6649 (tp) REVERT: C 257 MET cc_start: 0.8145 (mmm) cc_final: 0.7872 (mmt) REVERT: C 271 MET cc_start: 0.7599 (OUTLIER) cc_final: 0.7243 (mtm) REVERT: C 285 VAL cc_start: 0.8972 (t) cc_final: 0.7725 (p) REVERT: D 27 ARG cc_start: 0.4118 (OUTLIER) cc_final: 0.3690 (mtt-85) REVERT: D 138 MET cc_start: 0.7577 (mtp) cc_final: 0.6908 (tmm) REVERT: E 12 LEU cc_start: 0.8453 (tt) cc_final: 0.8103 (mp) REVERT: E 281 MET cc_start: 0.7569 (mmm) cc_final: 0.7234 (tpt) outliers start: 28 outliers final: 23 residues processed: 190 average time/residue: 0.2583 time to fit residues: 75.6704 Evaluate side-chains 176 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 151 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 89 HIS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 192 ASN Chi-restraints excluded: chain B residue 89 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 89 HIS Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 27 ARG Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 267 VAL Chi-restraints excluded: chain E residue 33 ILE Chi-restraints excluded: chain E residue 96 ASP Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 220 ILE Chi-restraints excluded: chain E residue 301 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 HIS ** D 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN ** E 45 ASN ** 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 = 0.4442 r_free = 0.4442 target = 0.197674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.169123 restraints weight = 21914.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.169163 restraints weight = 24471.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.171181 restraints weight = 19707.055| |-----------------------------------------------------------------------------| r_work (final): 0.4185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15720 Z= 0.209 Angle : 0.580 18.586 21315 Z= 0.284 Chirality : 0.039 0.196 2450 Planarity : 0.003 0.028 2620 Dihedral : 10.933 73.728 2590 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.10 % Allowed : 15.75 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.20), residues: 1880 helix: 1.40 (0.15), residues: 1172 sheet: 1.98 (0.60), residues: 68 loop : -0.68 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 260 HIS 0.004 0.001 HIS C 225 PHE 0.010 0.001 PHE D 226 TYR 0.014 0.001 TYR C 337 ARG 0.004 0.000 ARG B 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2913.08 seconds wall clock time: 54 minutes 59.13 seconds (3299.13 seconds total)