Starting phenix.real_space_refine on Sun Apr 14 15:10:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jay_36138/04_2024/8jay_36138.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jay_36138/04_2024/8jay_36138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jay_36138/04_2024/8jay_36138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jay_36138/04_2024/8jay_36138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jay_36138/04_2024/8jay_36138.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jay_36138/04_2024/8jay_36138.pdb" } resolution = 4.2 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= 0.025 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: 6 Type Number sf(0) Gaussians P 166 5.49 5 Mg 4 5.21 5 S 88 5.16 5 C 20152 2.51 5 N 5403 2.21 5 O 6169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 87": "OE1" <-> "OE2" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 79": "OE1" <-> "OE2" Residue "A TYR 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 119": "OD1" <-> "OD2" Residue "D TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 260": "OE1" <-> "OE2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 133": "OD1" <-> "OD2" Residue "J TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 8": "OE1" <-> "OE2" Residue "M TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 79": "OE1" <-> "OE2" Residue "M TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 31982 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3626 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 25, 'TRANS': 423} Chain breaks: 1 Chain: "A" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3618 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 25, 'TRANS': 422} Chain breaks: 1 Chain: "D" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3531 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 14, 'TRANS': 407} Chain: "B" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3531 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 14, 'TRANS': 407} Chain: "I" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3618 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 25, 'TRANS': 422} Chain breaks: 1 Chain: "J" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3531 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 14, 'TRANS': 407} Chain: "M" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3618 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 25, 'TRANS': 422} Chain breaks: 1 Chain: "N" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3531 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 14, 'TRANS': 407} Chain: "E" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 432 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "G" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "K" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "L" Number of atoms: 432 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "O" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.66, per 1000 atoms: 0.52 Number of scatterers: 31982 At special positions: 0 Unit cell: (119.34, 177.905, 233.155, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 88 16.00 P 166 15.00 Mg 4 11.99 O 6169 8.00 N 5403 7.00 C 20152 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: 13.86 Conformation dependent library (CDL) restraints added in 5.3 seconds 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6610 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 43 sheets defined 33.6% alpha, 11.2% beta 48 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 10.58 Creating SS restraints... Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 22 through 30 removed outlier: 3.994A pdb=" N GLY C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 60 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 109 through 132 removed outlier: 3.775A pdb=" N ARG C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 248 through 265 removed outlier: 4.009A pdb=" N ALA C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR C 258 " --> pdb=" O TRP C 254 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 351 removed outlier: 3.877A pdb=" N ALA C 335 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 376 removed outlier: 3.961A pdb=" N TRP C 370 " --> pdb=" O ASN C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 477 through 491 removed outlier: 3.957A pdb=" N ARG C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE C 489 " --> pdb=" O LYS C 485 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 507 removed outlier: 4.283A pdb=" N TYR C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 109 through 132 Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.492A pdb=" N GLN A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 225 through 230 removed outlier: 4.351A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 230' Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.558A pdb=" N GLY A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.964A pdb=" N SER A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 4.208A pdb=" N GLU A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.735A pdb=" N VAL A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 456 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.685A pdb=" N ARG A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 28 Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.820A pdb=" N ILE D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ARG D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 89 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.618A pdb=" N GLY D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 4.026A pdb=" N SER D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 257 through 279 removed outlier: 3.784A pdb=" N CYS D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 353 through 366 Processing helix chain 'D' and resid 369 through 385 Processing helix chain 'B' and resid 15 through 29 Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.681A pdb=" N ARG B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.133A pdb=" N PHE B 223 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 224 " --> pdb=" O TYR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 258 through 279 removed outlier: 3.611A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.678A pdb=" N LYS B 304 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 Processing helix chain 'B' and resid 369 through 385 Processing helix chain 'I' and resid 15 through 17 No H-bonds generated for 'chain 'I' and resid 15 through 17' Processing helix chain 'I' and resid 22 through 30 Processing helix chain 'I' and resid 46 through 61 removed outlier: 3.675A pdb=" N GLN I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 109 through 132 Processing helix chain 'I' and resid 206 through 215 removed outlier: 4.056A pdb=" N LEU I 210 " --> pdb=" O PHE I 206 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS I 211 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA I 212 " --> pdb=" O ASP I 208 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG I 213 " --> pdb=" O GLN I 209 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU I 214 " --> pdb=" O LEU I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 218 No H-bonds generated for 'chain 'I' and resid 216 through 218' Processing helix chain 'I' and resid 225 through 230 removed outlier: 4.149A pdb=" N LEU I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA I 230 " --> pdb=" O GLU I 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 225 through 230' Processing helix chain 'I' and resid 248 through 264 Processing helix chain 'I' and resid 331 through 351 removed outlier: 4.190A pdb=" N LYS I 336 " --> pdb=" O PRO I 332 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA I 337 " --> pdb=" O LYS I 333 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU I 338 " --> pdb=" O GLU I 334 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU I 339 " --> pdb=" O ALA I 335 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU I 344 " --> pdb=" O THR I 340 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER I 345 " --> pdb=" O GLN I 341 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR I 346 " --> pdb=" O ALA I 342 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN I 349 " --> pdb=" O SER I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 377 removed outlier: 4.111A pdb=" N TRP I 370 " --> pdb=" O ASN I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 461 removed outlier: 3.576A pdb=" N VAL I 455 " --> pdb=" O GLU I 451 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU I 460 " --> pdb=" O LEU I 456 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA I 461 " --> pdb=" O LYS I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 477 through 491 removed outlier: 3.817A pdb=" N ARG I 481 " --> pdb=" O PRO I 477 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU I 488 " --> pdb=" O ASN I 484 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE I 489 " --> pdb=" O LYS I 485 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 29 Processing helix chain 'J' and resid 44 through 56 removed outlier: 4.627A pdb=" N GLU J 50 " --> pdb=" O TRP J 46 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 70 removed outlier: 3.917A pdb=" N ASN J 69 " --> pdb=" O THR J 66 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS J 70 " --> pdb=" O ALA J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 89 removed outlier: 3.696A pdb=" N LEU J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 139 Processing helix chain 'J' and resid 152 through 157 removed outlier: 3.738A pdb=" N ILE J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 203 removed outlier: 3.659A pdb=" N THR J 202 " --> pdb=" O ASP J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 249 Processing helix chain 'J' and resid 258 through 278 removed outlier: 3.572A pdb=" N GLN J 262 " --> pdb=" O ASN J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 281 No H-bonds generated for 'chain 'J' and resid 279 through 281' Processing helix chain 'J' and resid 300 through 302 No H-bonds generated for 'chain 'J' and resid 300 through 302' Processing helix chain 'J' and resid 353 through 366 removed outlier: 3.788A pdb=" N GLN J 357 " --> pdb=" O SER J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 384 removed outlier: 3.744A pdb=" N LEU J 384 " --> pdb=" O PHE J 380 " (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 22 through 30 Processing helix chain 'M' and resid 46 through 61 removed outlier: 3.992A pdb=" N GLN M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 83 Processing helix chain 'M' and resid 109 through 132 removed outlier: 3.846A pdb=" N LEU M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 215 removed outlier: 3.739A pdb=" N LEU M 210 " --> pdb=" O PHE M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 265 removed outlier: 3.603A pdb=" N GLY M 265 " --> pdb=" O TYR M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 331 through 351 removed outlier: 3.902A pdb=" N LYS M 336 " --> pdb=" O PRO M 332 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA M 337 " --> pdb=" O LYS M 333 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER M 345 " --> pdb=" O GLN M 341 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR M 346 " --> pdb=" O ALA M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 Processing helix chain 'M' and resid 451 through 462 removed outlier: 3.594A pdb=" N VAL M 455 " --> pdb=" O GLU M 451 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU M 460 " --> pdb=" O LEU M 456 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 491 removed outlier: 3.870A pdb=" N ALA M 483 " --> pdb=" O THR M 479 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN M 484 " --> pdb=" O LEU M 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 28 Processing helix chain 'N' and resid 46 through 56 removed outlier: 3.525A pdb=" N GLU N 50 " --> pdb=" O TRP N 46 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE N 53 " --> pdb=" O ILE N 49 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ARG N 54 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 70 Processing helix chain 'N' and resid 71 through 89 removed outlier: 3.560A pdb=" N LEU N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 114 removed outlier: 4.507A pdb=" N ARG N 114 " --> pdb=" O ILE N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 138 Processing helix chain 'N' and resid 146 through 158 removed outlier: 4.327A pdb=" N SER N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 224 removed outlier: 3.828A pdb=" N PHE N 223 " --> pdb=" O GLU N 220 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE N 224 " --> pdb=" O TYR N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 248 Processing helix chain 'N' and resid 257 through 279 removed outlier: 3.870A pdb=" N CYS N 261 " --> pdb=" O ARG N 257 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP N 279 " --> pdb=" O LEU N 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 300 through 302 No H-bonds generated for 'chain 'N' and resid 300 through 302' Processing helix chain 'N' and resid 354 through 366 Processing helix chain 'N' and resid 369 through 385 Processing sheet with id=AA1, first strand: chain 'C' and resid 397 through 398 removed outlier: 3.707A pdb=" N LEU C 4 " --> pdb=" O PHE D 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'C' and resid 92 through 95 removed outlier: 6.727A pdb=" N VAL C 43 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY C 42 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE C 142 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 44 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP C 139 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU C 224 " --> pdb=" O TRP C 139 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL C 141 " --> pdb=" O LEU C 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 283 through 284 removed outlier: 4.048A pdb=" N VAL C 284 " --> pdb=" O CYS C 299 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 357 through 361 removed outlier: 7.100A pdb=" N VAL C 357 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL C 386 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 359 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE C 388 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA C 361 " --> pdb=" O ILE C 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 5 through 6 removed outlier: 5.872A pdb=" N ILE A 445 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR A 387 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 95 removed outlier: 7.256A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 6 removed outlier: 7.634A pdb=" N LYS D 4 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE D 60 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE D 6 " --> pdb=" O PHE D 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 63 through 64 removed outlier: 3.903A pdb=" N ALA D 98 " --> pdb=" O ILE D 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 207 through 208 removed outlier: 3.774A pdb=" N THR D 216 " --> pdb=" O ARG D 186 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG D 186 " --> pdb=" O THR D 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 283 through 285 Processing sheet with id=AB5, first strand: chain 'D' and resid 312 through 314 Processing sheet with id=AB6, first strand: chain 'D' and resid 390 through 393 Processing sheet with id=AB7, first strand: chain 'B' and resid 32 through 33 removed outlier: 5.848A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LYS B 4 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS B 59 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 61 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 8 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 63 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 98 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 177 Processing sheet with id=AB9, first strand: chain 'B' and resid 207 through 210 Processing sheet with id=AC1, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AC2, first strand: chain 'B' and resid 390 through 393 Processing sheet with id=AC3, first strand: chain 'I' and resid 5 through 6 removed outlier: 7.116A pdb=" N ILE I 359 " --> pdb=" O VAL I 386 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE I 388 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ALA I 361 " --> pdb=" O ILE I 388 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 12 through 14 removed outlier: 3.716A pdb=" N GLN I 18 " --> pdb=" O PHE I 14 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 93 through 95 removed outlier: 3.608A pdb=" N LYS I 94 " --> pdb=" O VAL I 43 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY I 45 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 397 through 398 Processing sheet with id=AC7, first strand: chain 'J' and resid 4 through 8 removed outlier: 7.725A pdb=" N LYS J 4 " --> pdb=" O CYS J 58 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE J 60 " --> pdb=" O LYS J 4 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE J 6 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE J 62 " --> pdb=" O PHE J 6 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER J 8 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER J 64 " --> pdb=" O SER J 8 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU J 97 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE J 62 " --> pdb=" O LEU J 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'J' and resid 175 through 177 Processing sheet with id=AC9, first strand: chain 'J' and resid 207 through 210 Processing sheet with id=AD1, first strand: chain 'J' and resid 283 through 285 Processing sheet with id=AD2, first strand: chain 'J' and resid 304 through 305 Processing sheet with id=AD3, first strand: chain 'J' and resid 390 through 391 Processing sheet with id=AD4, first strand: chain 'M' and resid 12 through 13 Processing sheet with id=AD5, first strand: chain 'M' and resid 91 through 95 removed outlier: 7.020A pdb=" N SER M 41 " --> pdb=" O VAL M 92 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LYS M 94 " --> pdb=" O SER M 41 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL M 43 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY M 42 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE M 142 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL M 44 " --> pdb=" O ILE M 142 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 278 through 279 removed outlier: 3.518A pdb=" N VAL M 357 " --> pdb=" O ASN M 382 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 360 through 361 removed outlier: 3.795A pdb=" N ILE M 388 " --> pdb=" O ALA M 361 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU M 444 " --> pdb=" O THR M 387 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.940A pdb=" N PHE N 6 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU N 61 " --> pdb=" O PHE N 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'N' and resid 63 through 64 Processing sheet with id=AE1, first strand: chain 'N' and resid 164 through 165 Processing sheet with id=AE2, first strand: chain 'N' and resid 169 through 172 Processing sheet with id=AE3, first strand: chain 'N' and resid 184 through 187 Processing sheet with id=AE4, first strand: chain 'N' and resid 283 through 286 removed outlier: 3.917A pdb=" N ARG N 283 " --> pdb=" O TRP N 294 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE N 291 " --> pdb=" O ALA N 325 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA N 325 " --> pdb=" O PHE N 291 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR N 293 " --> pdb=" O ILE N 323 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE N 323 " --> pdb=" O TYR N 293 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 283 through 286 removed outlier: 3.917A pdb=" N ARG N 283 " --> pdb=" O TRP N 294 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE N 291 " --> pdb=" O ALA N 325 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA N 325 " --> pdb=" O PHE N 291 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR N 293 " --> pdb=" O ILE N 323 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE N 323 " --> pdb=" O TYR N 293 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 304 through 305 Processing sheet with id=AE7, first strand: chain 'N' and resid 390 through 394 917 hydrogen bonds defined for protein. 2553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 119 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 11.47 Time building geometry restraints manager: 14.67 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: 8342 1.33 - 1.45: 7103 1.45 - 1.57: 17203 1.57 - 1.69: 324 1.69 - 1.81: 136 Bond restraints: 33108 Sorted by residual: bond pdb=" CD GLU C 344 " pdb=" OE1 GLU C 344 " ideal model delta sigma weight residual 1.249 1.219 0.030 1.90e-02 2.77e+03 2.49e+00 bond pdb=" CB GLN C 430 " pdb=" CG GLN C 430 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CB ARG C 243 " pdb=" CG ARG C 243 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CA GLN C 430 " pdb=" CB GLN C 430 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.69e+00 bond pdb=" C3' DC L 19 " pdb=" O3' DC L 19 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.66e+00 ... (remaining 33103 not shown) Histogram of bond angle deviations from ideal: 97.56 - 104.92: 1112 104.92 - 112.28: 16588 112.28 - 119.64: 11411 119.64 - 126.99: 15527 126.99 - 134.35: 787 Bond angle restraints: 45425 Sorted by residual: angle pdb=" N GLU C 344 " pdb=" CA GLU C 344 " pdb=" CB GLU C 344 " ideal model delta sigma weight residual 110.28 117.45 -7.17 1.55e+00 4.16e-01 2.14e+01 angle pdb=" N ILE D 348 " pdb=" CA ILE D 348 " pdb=" C ILE D 348 " ideal model delta sigma weight residual 112.96 108.65 4.31 1.00e+00 1.00e+00 1.86e+01 angle pdb=" CA LEU D 39 " pdb=" CB LEU D 39 " pdb=" CG LEU D 39 " ideal model delta sigma weight residual 116.30 128.72 -12.42 3.50e+00 8.16e-02 1.26e+01 angle pdb=" CA GLN C 430 " pdb=" CB GLN C 430 " pdb=" CG GLN C 430 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" C LEU C 343 " pdb=" N GLU C 344 " pdb=" CA GLU C 344 " ideal model delta sigma weight residual 120.31 115.04 5.27 1.52e+00 4.33e-01 1.20e+01 ... (remaining 45420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.11: 18808 34.11 - 68.23: 775 68.23 - 102.34: 42 102.34 - 136.45: 7 136.45 - 170.57: 5 Dihedral angle restraints: 19637 sinusoidal: 9410 harmonic: 10227 Sorted by residual: dihedral pdb=" CA MET J 92 " pdb=" C MET J 92 " pdb=" N PHE J 93 " pdb=" CA PHE J 93 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ILE C 242 " pdb=" C ILE C 242 " pdb=" N ARG C 243 " pdb=" CA ARG C 243 " ideal model delta harmonic sigma weight residual -180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA TYR J 210 " pdb=" C TYR J 210 " pdb=" N LYS J 211 " pdb=" CA LYS J 211 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 19634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 3579 0.043 - 0.086: 970 0.086 - 0.129: 321 0.129 - 0.172: 29 0.172 - 0.215: 10 Chirality restraints: 4909 Sorted by residual: chirality pdb=" C1' U K 15 " pdb=" O4' U K 15 " pdb=" C2' U K 15 " pdb=" N1 U K 15 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE J 157 " pdb=" CA ILE J 157 " pdb=" CG1 ILE J 157 " pdb=" CG2 ILE J 157 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" P U O 1 " pdb=" OP1 U O 1 " pdb=" OP2 U O 1 " pdb=" O5' U O 1 " both_signs ideal model delta sigma weight residual True 2.17 2.38 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 4906 not shown) Planarity restraints: 5180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 231 " -0.025 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP C 231 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP C 231 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP C 231 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP C 231 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 231 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 231 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 231 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 231 " -0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP C 231 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 361 " 0.246 9.50e-02 1.11e+02 1.10e-01 7.45e+00 pdb=" NE ARG D 361 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG D 361 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 361 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 361 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 439 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO I 440 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO I 440 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 440 " -0.031 5.00e-02 4.00e+02 ... (remaining 5177 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 397 2.58 - 3.16: 26425 3.16 - 3.74: 51620 3.74 - 4.32: 65572 4.32 - 4.90: 103021 Nonbonded interactions: 247035 Sorted by model distance: nonbonded pdb=" OP1 A E 3 " pdb="MG MG E 101 " model vdw 1.999 2.170 nonbonded pdb=" OP1 A K 3 " pdb="MG MG K 101 " model vdw 2.000 2.170 nonbonded pdb=" OP3 U K 1 " pdb="MG MG K 101 " model vdw 2.033 2.170 nonbonded pdb=" OP3 U O 1 " pdb="MG MG M 601 " model vdw 2.051 2.170 nonbonded pdb=" OP2 U G 1 " pdb="MG MG G 101 " model vdw 2.086 2.170 ... (remaining 247030 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 'C' and (resid 1 through 144 or resid 204 through 507)) selection = chain 'I' selection = (chain 'M' and resid 1 through 507) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'J' selection = chain 'N' } ncs_group { reference = (chain 'E' and resid 1 through 21) selection = (chain 'G' and resid 1 through 21) selection = (chain 'K' and resid 1 through 21) selection = chain 'O' } ncs_group { reference = (chain 'F' and resid 4 through 23) selection = chain 'H' selection = (chain 'L' and resid 4 through 23) selection = chain 'P' } 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=0.67 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: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 18.500 Check model and map are aligned: 0.510 Set scattering table: 0.340 Process input model: 90.730 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.210 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.003 0.043 33108 Z= 0.168 Angle : 0.651 12.423 45425 Z= 0.337 Chirality : 0.044 0.215 4909 Planarity : 0.004 0.110 5180 Dihedral : 17.448 170.565 13027 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3457 helix: 0.61 (0.17), residues: 1002 sheet: -1.24 (0.21), residues: 601 loop : -2.28 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP C 231 HIS 0.006 0.001 HIS N 188 PHE 0.035 0.001 PHE C 245 TYR 0.019 0.001 TYR B 213 ARG 0.015 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 3.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ILE cc_start: 0.8370 (mm) cc_final: 0.8153 (tp) REVERT: C 324 GLU cc_start: 0.6758 (tp30) cc_final: 0.6533 (tp30) REVERT: C 503 PHE cc_start: 0.4778 (m-10) cc_final: 0.4241 (m-80) REVERT: A 111 HIS cc_start: 0.8172 (p-80) cc_final: 0.7638 (m-70) REVERT: A 489 ILE cc_start: 0.9344 (pt) cc_final: 0.9062 (pt) REVERT: D 14 ASP cc_start: 0.7969 (p0) cc_final: 0.7100 (p0) REVERT: D 193 ARG cc_start: 0.6354 (tpt170) cc_final: 0.5866 (tpt170) REVERT: D 215 CYS cc_start: 0.6942 (m) cc_final: 0.6728 (m) REVERT: D 268 LEU cc_start: 0.8669 (mm) cc_final: 0.8403 (pp) REVERT: D 277 MET cc_start: 0.8256 (tmm) cc_final: 0.8040 (ppp) REVERT: D 336 MET cc_start: 0.7330 (mmp) cc_final: 0.6643 (mmp) REVERT: I 280 TYR cc_start: 0.7840 (m-10) cc_final: 0.7514 (m-10) REVERT: I 304 PHE cc_start: 0.8492 (t80) cc_final: 0.8110 (t80) REVERT: J 262 GLN cc_start: 0.8685 (mp10) cc_final: 0.8314 (mp10) REVERT: J 294 TRP cc_start: 0.5750 (p-90) cc_final: 0.5144 (p-90) REVERT: J 336 MET cc_start: 0.7383 (pmm) cc_final: 0.7026 (pmm) REVERT: J 411 PHE cc_start: 0.7901 (p90) cc_final: 0.7684 (p90) REVERT: M 370 TRP cc_start: 0.6854 (t-100) cc_final: 0.6450 (t-100) REVERT: N 260 GLU cc_start: 0.6309 (pm20) cc_final: 0.5936 (mt-10) REVERT: N 271 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7822 (mmtt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.4397 time to fit residues: 267.1366 Evaluate side-chains 265 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 3.382 ------------------------------------------------------------------------------- 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: 10.0000 chunk 272 optimal weight: 6.9990 chunk 151 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 184 optimal weight: 6.9990 chunk 145 optimal weight: 0.6980 chunk 282 optimal weight: 6.9990 chunk 109 optimal weight: 0.0270 chunk 171 optimal weight: 9.9990 chunk 210 optimal weight: 0.6980 chunk 326 optimal weight: 10.0000 overall best weight: 1.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 18 GLN C 207 HIS C 302 GLN C 430 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN ** M 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 329 HIS M 374 ASN ** N 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 33108 Z= 0.212 Angle : 0.617 10.099 45425 Z= 0.317 Chirality : 0.044 0.240 4909 Planarity : 0.004 0.049 5180 Dihedral : 17.077 169.939 5785 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 0.16 % Allowed : 6.24 % Favored : 93.60 % 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: -1.81 (0.14), residues: 3457 helix: 0.54 (0.16), residues: 1029 sheet: -1.34 (0.21), residues: 619 loop : -2.26 (0.14), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 192 HIS 0.006 0.001 HIS J 358 PHE 0.019 0.001 PHE I 403 TYR 0.032 0.001 TYR B 213 ARG 0.032 0.001 ARG A 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 343 time to evaluate : 3.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ILE cc_start: 0.8488 (mm) cc_final: 0.8121 (tp) REVERT: C 503 PHE cc_start: 0.5343 (m-10) cc_final: 0.4919 (m-80) REVERT: A 430 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8573 (tm-30) REVERT: D 14 ASP cc_start: 0.8014 (p0) cc_final: 0.7342 (p0) REVERT: D 133 ASP cc_start: 0.9127 (p0) cc_final: 0.8805 (p0) REVERT: D 277 MET cc_start: 0.8253 (tmm) cc_final: 0.7991 (ppp) REVERT: D 323 ILE cc_start: 0.6704 (pt) cc_final: 0.6280 (pt) REVERT: B 151 ASN cc_start: 0.7774 (p0) cc_final: 0.7506 (p0) REVERT: I 1 MET cc_start: 0.8433 (mpp) cc_final: 0.7847 (mmm) REVERT: J 262 GLN cc_start: 0.8774 (mp10) cc_final: 0.8355 (mp10) REVERT: J 294 TRP cc_start: 0.6067 (p-90) cc_final: 0.5161 (p-90) REVERT: J 336 MET cc_start: 0.7468 (pmm) cc_final: 0.7072 (pmm) REVERT: J 411 PHE cc_start: 0.8053 (p90) cc_final: 0.7823 (p90) REVERT: M 89 GLN cc_start: 0.8950 (mm-40) cc_final: 0.8686 (mm110) REVERT: N 271 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7816 (mmtt) outliers start: 5 outliers final: 1 residues processed: 348 average time/residue: 0.4222 time to fit residues: 240.6542 Evaluate side-chains 261 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 259 time to evaluate : 3.330 ------------------------------------------------------------------------------- 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: 4.9990 chunk 101 optimal weight: 0.6980 chunk 272 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 327 optimal weight: 10.0000 chunk 353 optimal weight: 10.0000 chunk 291 optimal weight: 0.7980 chunk 324 optimal weight: 0.0980 chunk 111 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS C 430 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 295 GLN M 374 ASN N 116 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 33108 Z= 0.256 Angle : 0.646 10.413 45425 Z= 0.331 Chirality : 0.045 0.291 4909 Planarity : 0.004 0.073 5180 Dihedral : 17.130 170.889 5785 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.89 % Favored : 90.11 % Rotamer: Outliers : 0.06 % Allowed : 5.92 % Favored : 94.02 % 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: -1.92 (0.14), residues: 3457 helix: 0.44 (0.16), residues: 1037 sheet: -1.45 (0.21), residues: 601 loop : -2.32 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 192 HIS 0.014 0.001 HIS D 358 PHE 0.037 0.002 PHE A 403 TYR 0.025 0.002 TYR M 346 ARG 0.014 0.001 ARG D 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 333 time to evaluate : 3.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ILE cc_start: 0.8342 (mm) cc_final: 0.8059 (tp) REVERT: C 303 MET cc_start: 0.8054 (ptm) cc_final: 0.7801 (ptm) REVERT: D 133 ASP cc_start: 0.9059 (p0) cc_final: 0.8838 (p0) REVERT: D 165 ILE cc_start: 0.8672 (mt) cc_final: 0.8429 (mt) REVERT: D 277 MET cc_start: 0.8286 (tmm) cc_final: 0.7959 (tmm) REVERT: B 137 LYS cc_start: 0.8030 (ptmm) cc_final: 0.7749 (pptt) REVERT: B 151 ASN cc_start: 0.7813 (p0) cc_final: 0.7580 (p0) REVERT: B 192 TRP cc_start: 0.7129 (p-90) cc_final: 0.6427 (p90) REVERT: B 349 ASN cc_start: 0.8693 (t0) cc_final: 0.8098 (p0) REVERT: I 304 PHE cc_start: 0.8735 (t80) cc_final: 0.8439 (t80) REVERT: J 262 GLN cc_start: 0.8719 (mp10) cc_final: 0.8338 (mp10) REVERT: J 336 MET cc_start: 0.7463 (pmm) cc_final: 0.7093 (pmm) REVERT: N 271 LYS cc_start: 0.8202 (mmtt) cc_final: 0.7813 (mmtt) outliers start: 2 outliers final: 1 residues processed: 335 average time/residue: 0.4247 time to fit residues: 232.1283 Evaluate side-chains 244 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 243 time to evaluate : 3.698 ------------------------------------------------------------------------------- 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: 0.7980 chunk 246 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 156 optimal weight: 5.9990 chunk 219 optimal weight: 3.9990 chunk 328 optimal weight: 0.9990 chunk 347 optimal weight: 6.9990 chunk 171 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 302 GLN C 360 HIS C 430 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 ASN I 382 ASN ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 251 HIS M 374 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33108 Z= 0.227 Angle : 0.628 10.460 45425 Z= 0.323 Chirality : 0.045 0.289 4909 Planarity : 0.004 0.048 5180 Dihedral : 17.109 170.607 5785 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 0.03 % Allowed : 4.82 % Favored : 95.14 % 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: -1.92 (0.14), residues: 3457 helix: 0.47 (0.16), residues: 1035 sheet: -1.52 (0.21), residues: 597 loop : -2.31 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 192 HIS 0.007 0.001 HIS J 358 PHE 0.020 0.002 PHE C 425 TYR 0.017 0.002 TYR M 346 ARG 0.005 0.000 ARG D 263 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 333 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ILE cc_start: 0.8439 (mm) cc_final: 0.8075 (tp) REVERT: C 303 MET cc_start: 0.8059 (ptm) cc_final: 0.7812 (ptm) REVERT: A 225 ARG cc_start: 0.6634 (mpt-90) cc_final: 0.6223 (mtt90) REVERT: D 74 VAL cc_start: 0.8674 (m) cc_final: 0.8326 (p) REVERT: D 165 ILE cc_start: 0.8638 (mt) cc_final: 0.8398 (mt) REVERT: D 277 MET cc_start: 0.8232 (tmm) cc_final: 0.7837 (tmm) REVERT: D 323 ILE cc_start: 0.6602 (pt) cc_final: 0.6263 (pt) REVERT: B 151 ASN cc_start: 0.7703 (p0) cc_final: 0.7450 (p0) REVERT: B 349 ASN cc_start: 0.8695 (t0) cc_final: 0.8109 (p0) REVERT: J 262 GLN cc_start: 0.8710 (mp10) cc_final: 0.8348 (mp10) REVERT: J 336 MET cc_start: 0.7442 (pmm) cc_final: 0.7070 (pmm) outliers start: 1 outliers final: 0 residues processed: 334 average time/residue: 0.4196 time to fit residues: 228.8694 Evaluate side-chains 246 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 3.674 ------------------------------------------------------------------------------- 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: 0.5980 chunk 197 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 259 optimal weight: 7.9990 chunk 143 optimal weight: 0.6980 chunk 296 optimal weight: 3.9990 chunk 240 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 177 optimal weight: 6.9990 chunk 312 optimal weight: 9.9990 chunk 87 optimal weight: 7.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 430 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 HIS ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 251 HIS M 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33108 Z= 0.220 Angle : 0.631 10.834 45425 Z= 0.323 Chirality : 0.045 0.287 4909 Planarity : 0.004 0.078 5180 Dihedral : 17.114 170.667 5785 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.79 % 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: -1.91 (0.14), residues: 3457 helix: 0.57 (0.16), residues: 1014 sheet: -1.54 (0.21), residues: 590 loop : -2.32 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 319 HIS 0.009 0.001 HIS D 320 PHE 0.019 0.002 PHE C 425 TYR 0.019 0.001 TYR C 346 ARG 0.019 0.001 ARG D 361 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 343 time to evaluate : 3.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.2818 (tpt) cc_final: 0.1896 (tpt) REVERT: C 36 ILE cc_start: 0.8460 (mm) cc_final: 0.8152 (mm) REVERT: C 303 MET cc_start: 0.8015 (ptm) cc_final: 0.7776 (ptm) REVERT: A 225 ARG cc_start: 0.6520 (mpt-90) cc_final: 0.6172 (mtt90) REVERT: A 353 TYR cc_start: 0.7287 (m-80) cc_final: 0.7001 (m-80) REVERT: D 165 ILE cc_start: 0.8513 (mt) cc_final: 0.8270 (mt) REVERT: D 323 ILE cc_start: 0.6599 (pt) cc_final: 0.6206 (pt) REVERT: D 401 ILE cc_start: 0.8663 (mt) cc_final: 0.8409 (mm) REVERT: B 151 ASN cc_start: 0.7671 (p0) cc_final: 0.7447 (p0) REVERT: B 349 ASN cc_start: 0.8716 (t0) cc_final: 0.8150 (p0) REVERT: J 251 TYR cc_start: 0.6144 (t80) cc_final: 0.5796 (t80) REVERT: J 262 GLN cc_start: 0.8685 (mp10) cc_final: 0.8391 (mp10) REVERT: J 336 MET cc_start: 0.7422 (pmm) cc_final: 0.7050 (pmm) REVERT: N 50 GLU cc_start: 0.8345 (tm-30) cc_final: 0.8081 (tm-30) outliers start: 1 outliers final: 0 residues processed: 344 average time/residue: 0.4219 time to fit residues: 237.1460 Evaluate side-chains 255 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 3.477 ------------------------------------------------------------------------------- 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: 10.0000 chunk 313 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 204 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 348 optimal weight: 7.9990 chunk 289 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 ASN C 302 GLN ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33108 Z= 0.242 Angle : 0.654 11.278 45425 Z= 0.335 Chirality : 0.046 0.285 4909 Planarity : 0.004 0.070 5180 Dihedral : 17.147 170.738 5785 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 0.03 % Allowed : 3.15 % Favored : 96.82 % 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: -1.99 (0.14), residues: 3457 helix: 0.45 (0.16), residues: 1028 sheet: -1.58 (0.21), residues: 590 loop : -2.35 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP B 192 HIS 0.009 0.001 HIS J 358 PHE 0.031 0.002 PHE I 403 TYR 0.032 0.002 TYR C 37 ARG 0.015 0.001 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 3.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.2887 (tpt) cc_final: 0.2209 (tpt) REVERT: C 36 ILE cc_start: 0.8381 (mm) cc_final: 0.8120 (mm) REVERT: A 225 ARG cc_start: 0.6555 (mpt-90) cc_final: 0.6092 (mtt90) REVERT: A 353 TYR cc_start: 0.7356 (m-80) cc_final: 0.7069 (m-80) REVERT: A 430 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8443 (tm-30) REVERT: D 74 VAL cc_start: 0.8613 (m) cc_final: 0.8280 (p) REVERT: D 99 ILE cc_start: 0.8771 (pt) cc_final: 0.8278 (mt) REVERT: D 165 ILE cc_start: 0.8515 (mt) cc_final: 0.8267 (mt) REVERT: D 209 ARG cc_start: 0.6902 (mmt90) cc_final: 0.6459 (mmt90) REVERT: D 215 CYS cc_start: 0.6433 (m) cc_final: 0.6228 (m) REVERT: D 401 ILE cc_start: 0.8659 (mt) cc_final: 0.8397 (mm) REVERT: B 349 ASN cc_start: 0.8784 (t0) cc_final: 0.8194 (p0) REVERT: J 251 TYR cc_start: 0.6227 (t80) cc_final: 0.5884 (t80) REVERT: J 262 GLN cc_start: 0.8606 (mp10) cc_final: 0.8283 (mp10) REVERT: J 336 MET cc_start: 0.7442 (pmm) cc_final: 0.7081 (pmm) outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 0.4141 time to fit residues: 225.5437 Evaluate side-chains 252 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 3.611 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 1.9990 chunk 198 optimal weight: 0.0970 chunk 254 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 293 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 346 optimal weight: 10.0000 chunk 217 optimal weight: 3.9990 chunk 211 optimal weight: 0.4980 chunk 160 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN C 302 GLN C 430 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 HIS ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 251 HIS M 374 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33108 Z= 0.169 Angle : 0.619 11.491 45425 Z= 0.315 Chirality : 0.045 0.237 4909 Planarity : 0.004 0.060 5180 Dihedral : 17.044 170.337 5785 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.48 % Favored : 91.50 % Rotamer: Outliers : 0.03 % Allowed : 2.16 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.84 (0.14), residues: 3457 helix: 0.58 (0.16), residues: 1027 sheet: -1.44 (0.21), residues: 589 loop : -2.30 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 33 HIS 0.009 0.001 HIS J 358 PHE 0.028 0.001 PHE D 60 TYR 0.028 0.001 TYR B 213 ARG 0.004 0.000 ARG D 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 356 time to evaluate : 3.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ILE cc_start: 0.8292 (mm) cc_final: 0.8051 (mm) REVERT: C 406 MET cc_start: 0.8245 (tmm) cc_final: 0.7956 (tmm) REVERT: A 225 ARG cc_start: 0.6396 (mpt-90) cc_final: 0.6003 (mtt90) REVERT: A 411 TYR cc_start: 0.7953 (t80) cc_final: 0.7674 (t80) REVERT: D 74 VAL cc_start: 0.8636 (m) cc_final: 0.8308 (p) REVERT: D 99 ILE cc_start: 0.8716 (pt) cc_final: 0.8078 (mt) REVERT: D 215 CYS cc_start: 0.6365 (m) cc_final: 0.6154 (m) REVERT: D 277 MET cc_start: 0.8078 (ppp) cc_final: 0.7665 (ppp) REVERT: D 323 ILE cc_start: 0.6412 (pt) cc_final: 0.6044 (pt) REVERT: D 401 ILE cc_start: 0.8657 (mt) cc_final: 0.8350 (mm) REVERT: B 151 ASN cc_start: 0.7771 (p0) cc_final: 0.7542 (p0) REVERT: B 349 ASN cc_start: 0.8743 (t0) cc_final: 0.8160 (p0) REVERT: I 280 TYR cc_start: 0.8082 (m-80) cc_final: 0.7801 (m-10) REVERT: I 303 MET cc_start: 0.7538 (tpp) cc_final: 0.7125 (tpt) REVERT: J 251 TYR cc_start: 0.5980 (t80) cc_final: 0.5691 (t80) REVERT: J 262 GLN cc_start: 0.8596 (mp10) cc_final: 0.8349 (mp10) REVERT: J 336 MET cc_start: 0.7598 (pmm) cc_final: 0.7240 (pmm) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.4283 time to fit residues: 251.5877 Evaluate side-chains 249 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 3.878 ------------------------------------------------------------------------------- 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: 6.9990 chunk 138 optimal weight: 0.4980 chunk 207 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 67 optimal weight: 0.0980 chunk 220 optimal weight: 0.6980 chunk 236 optimal weight: 4.9990 chunk 171 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 382 ASN ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS M 295 GLN M 374 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33108 Z= 0.238 Angle : 0.655 11.660 45425 Z= 0.335 Chirality : 0.046 0.257 4909 Planarity : 0.004 0.068 5180 Dihedral : 17.122 170.841 5785 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.38 % Favored : 89.59 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.92 (0.14), residues: 3457 helix: 0.51 (0.16), residues: 1029 sheet: -1.48 (0.21), residues: 581 loop : -2.34 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 192 HIS 0.009 0.001 HIS J 358 PHE 0.029 0.002 PHE I 403 TYR 0.025 0.002 TYR B 213 ARG 0.005 0.000 ARG D 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 3.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ILE cc_start: 0.8379 (mm) cc_final: 0.8085 (mm) REVERT: A 225 ARG cc_start: 0.6491 (mpt-90) cc_final: 0.6067 (mtt90) REVERT: A 411 TYR cc_start: 0.7985 (t80) cc_final: 0.7689 (t80) REVERT: D 74 VAL cc_start: 0.8678 (m) cc_final: 0.8355 (p) REVERT: D 92 MET cc_start: 0.7773 (ttp) cc_final: 0.7554 (ttp) REVERT: D 99 ILE cc_start: 0.8762 (pt) cc_final: 0.8491 (mt) REVERT: D 100 ASP cc_start: 0.7540 (t0) cc_final: 0.7006 (t0) REVERT: D 133 ASP cc_start: 0.9139 (p0) cc_final: 0.8938 (p0) REVERT: D 165 ILE cc_start: 0.8532 (mt) cc_final: 0.8256 (mt) REVERT: D 215 CYS cc_start: 0.6392 (m) cc_final: 0.6153 (m) REVERT: D 277 MET cc_start: 0.8297 (ppp) cc_final: 0.7912 (ppp) REVERT: D 323 ILE cc_start: 0.6527 (pt) cc_final: 0.6180 (pt) REVERT: D 401 ILE cc_start: 0.8681 (mt) cc_final: 0.8365 (mm) REVERT: B 151 ASN cc_start: 0.7888 (p0) cc_final: 0.7616 (p0) REVERT: B 349 ASN cc_start: 0.8761 (t0) cc_final: 0.8162 (p0) REVERT: I 243 ARG cc_start: 0.6168 (mtp180) cc_final: 0.5563 (mtp180) REVERT: I 303 MET cc_start: 0.7806 (tpp) cc_final: 0.7439 (tpt) REVERT: J 251 TYR cc_start: 0.6102 (t80) cc_final: 0.5876 (t80) REVERT: J 262 GLN cc_start: 0.8667 (mp10) cc_final: 0.8372 (mp10) REVERT: J 336 MET cc_start: 0.7594 (pmm) cc_final: 0.7223 (pmm) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.4143 time to fit residues: 226.3299 Evaluate side-chains 254 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 4.261 ------------------------------------------------------------------------------- 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: 0.9990 chunk 332 optimal weight: 0.5980 chunk 303 optimal weight: 0.0060 chunk 323 optimal weight: 9.9990 chunk 194 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 chunk 253 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 292 optimal weight: 3.9990 chunk 305 optimal weight: 4.9990 chunk 322 optimal weight: 9.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 90 ASN ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33108 Z= 0.160 Angle : 0.624 11.980 45425 Z= 0.315 Chirality : 0.045 0.243 4909 Planarity : 0.004 0.082 5180 Dihedral : 16.988 170.554 5785 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.58 % Favored : 92.36 % Rotamer: Outliers : 0.03 % Allowed : 0.58 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.14), residues: 3457 helix: 0.56 (0.16), residues: 1033 sheet: -1.30 (0.21), residues: 593 loop : -2.27 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 192 HIS 0.010 0.001 HIS J 358 PHE 0.021 0.001 PHE M 93 TYR 0.028 0.001 TYR B 213 ARG 0.017 0.000 ARG J 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 347 time to evaluate : 3.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ILE cc_start: 0.8224 (mm) cc_final: 0.8016 (mm) REVERT: C 134 GLU cc_start: 0.8620 (mp0) cc_final: 0.8366 (mp0) REVERT: A 111 HIS cc_start: 0.8090 (p-80) cc_final: 0.7504 (m-70) REVERT: A 225 ARG cc_start: 0.6354 (mpt-90) cc_final: 0.5953 (mtt90) REVERT: D 74 VAL cc_start: 0.8609 (m) cc_final: 0.8273 (p) REVERT: D 92 MET cc_start: 0.7737 (ttp) cc_final: 0.7498 (ttp) REVERT: D 99 ILE cc_start: 0.8722 (pt) cc_final: 0.8470 (mt) REVERT: D 100 ASP cc_start: 0.7583 (t0) cc_final: 0.7069 (t0) REVERT: D 133 ASP cc_start: 0.9128 (p0) cc_final: 0.8920 (p0) REVERT: D 215 CYS cc_start: 0.6249 (m) cc_final: 0.6013 (m) REVERT: D 277 MET cc_start: 0.8408 (ppp) cc_final: 0.8067 (ppp) REVERT: D 323 ILE cc_start: 0.6388 (pt) cc_final: 0.6010 (pt) REVERT: D 401 ILE cc_start: 0.8588 (mt) cc_final: 0.8260 (mm) REVERT: B 151 ASN cc_start: 0.7788 (p0) cc_final: 0.7583 (p0) REVERT: B 349 ASN cc_start: 0.8708 (t0) cc_final: 0.8153 (p0) REVERT: I 303 MET cc_start: 0.7456 (tpp) cc_final: 0.7122 (tpt) REVERT: J 190 TYR cc_start: 0.4666 (t80) cc_final: 0.4421 (t80) REVERT: J 262 GLN cc_start: 0.8586 (mp10) cc_final: 0.8330 (mp10) REVERT: J 336 MET cc_start: 0.7569 (pmm) cc_final: 0.7174 (pmm) outliers start: 1 outliers final: 0 residues processed: 347 average time/residue: 0.4115 time to fit residues: 235.8254 Evaluate side-chains 260 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 3.731 ------------------------------------------------------------------------------- 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: 2.9990 chunk 341 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 162 optimal weight: 0.0170 chunk 237 optimal weight: 3.9990 chunk 358 optimal weight: 10.0000 chunk 330 optimal weight: 4.9990 chunk 285 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 220 optimal weight: 0.9990 chunk 175 optimal weight: 0.4980 overall best weight: 1.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33108 Z= 0.178 Angle : 0.631 12.349 45425 Z= 0.318 Chirality : 0.045 0.250 4909 Planarity : 0.004 0.056 5180 Dihedral : 16.999 170.996 5785 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 8.82 % Favored : 91.12 % Rotamer: Outliers : 0.03 % Allowed : 0.42 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.77 (0.14), residues: 3457 helix: 0.61 (0.16), residues: 1029 sheet: -1.25 (0.21), residues: 590 loop : -2.28 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 192 HIS 0.011 0.001 HIS J 358 PHE 0.027 0.001 PHE A 403 TYR 0.025 0.001 TYR B 213 ARG 0.008 0.000 ARG C 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 330 time to evaluate : 3.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 GLU cc_start: 0.7458 (tp30) cc_final: 0.7015 (tp30) REVERT: A 225 ARG cc_start: 0.6419 (mpt-90) cc_final: 0.5997 (mtt90) REVERT: A 411 TYR cc_start: 0.7886 (t80) cc_final: 0.7649 (t80) REVERT: D 34 CYS cc_start: 0.8529 (t) cc_final: 0.8204 (t) REVERT: D 92 MET cc_start: 0.7753 (ttp) cc_final: 0.7517 (ttp) REVERT: D 99 ILE cc_start: 0.8743 (pt) cc_final: 0.8469 (mt) REVERT: D 100 ASP cc_start: 0.7503 (t0) cc_final: 0.7032 (t0) REVERT: D 215 CYS cc_start: 0.6290 (m) cc_final: 0.6051 (m) REVERT: D 277 MET cc_start: 0.8421 (ppp) cc_final: 0.8077 (ppp) REVERT: D 323 ILE cc_start: 0.6512 (pt) cc_final: 0.6167 (pt) REVERT: D 401 ILE cc_start: 0.8608 (mt) cc_final: 0.8275 (mm) REVERT: B 151 ASN cc_start: 0.7771 (p0) cc_final: 0.7558 (p0) REVERT: B 349 ASN cc_start: 0.8711 (t0) cc_final: 0.8152 (p0) REVERT: I 303 MET cc_start: 0.7604 (tpp) cc_final: 0.7287 (tpt) REVERT: J 262 GLN cc_start: 0.8635 (mp10) cc_final: 0.8382 (mp10) REVERT: J 336 MET cc_start: 0.7623 (pmm) cc_final: 0.7222 (pmm) REVERT: N 122 LYS cc_start: 0.7587 (mmtm) cc_final: 0.7334 (mmtm) outliers start: 1 outliers final: 0 residues processed: 330 average time/residue: 0.4168 time to fit residues: 229.1772 Evaluate side-chains 256 residues out of total 3109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 3.733 ------------------------------------------------------------------------------- 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: 0.1980 chunk 304 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 263 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 286 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 293 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 52 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.105786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.086833 restraints weight = 122438.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.088572 restraints weight = 78578.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.089743 restraints weight = 58500.344| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33108 Z= 0.152 Angle : 0.618 12.484 45425 Z= 0.310 Chirality : 0.044 0.241 4909 Planarity : 0.004 0.052 5180 Dihedral : 16.913 171.080 5785 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.23 % Favored : 92.71 % Rotamer: Outliers : 0.03 % Allowed : 0.61 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.14), residues: 3457 helix: 0.68 (0.16), residues: 1028 sheet: -1.17 (0.21), residues: 603 loop : -2.22 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP B 192 HIS 0.011 0.001 HIS J 358 PHE 0.024 0.001 PHE A 403 TYR 0.026 0.001 TYR B 213 ARG 0.007 0.000 ARG C 243 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6022.09 seconds wall clock time: 112 minutes 26.05 seconds (6746.05 seconds total)