Starting phenix.real_space_refine on Wed Feb 14 14:31:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xec_33155/02_2024/7xec_33155_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xec_33155/02_2024/7xec_33155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xec_33155/02_2024/7xec_33155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xec_33155/02_2024/7xec_33155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xec_33155/02_2024/7xec_33155_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xec_33155/02_2024/7xec_33155_updated.pdb" } resolution = 3.34 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= -0.001 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 43 5.16 5 C 6074 2.51 5 N 1670 2.21 5 O 1695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 104": "NH1" <-> "NH2" Residue "A TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 117": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 124": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 152": "NH1" <-> "NH2" Residue "A ARG 165": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 259": "NH1" <-> "NH2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 274": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 285": "NH1" <-> "NH2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 545": "NH1" <-> "NH2" Residue "A ARG 568": "NH1" <-> "NH2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A ARG 622": "NH1" <-> "NH2" Residue "A GLU 640": "OE1" <-> "OE2" Residue "A TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 89": "NH1" <-> "NH2" Residue "B ARG 104": "NH1" <-> "NH2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B ARG 117": "NH1" <-> "NH2" Residue "B ARG 120": "NH1" <-> "NH2" Residue "B ARG 124": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B ARG 165": "NH1" <-> "NH2" Residue "B TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ASP 187": "OD1" <-> "OD2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 236": "NH1" <-> "NH2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 271": "OE1" <-> "OE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B ARG 275": "NH1" <-> "NH2" Residue "B GLU 278": "OE1" <-> "OE2" Residue "B ARG 280": "NH1" <-> "NH2" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 285": "NH1" <-> "NH2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 371": "OE1" <-> "OE2" Residue "B PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B TYR 406": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 408": "OE1" <-> "OE2" Residue "B TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 496": "NH1" <-> "NH2" Residue "B TYR 527": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 545": "NH1" <-> "NH2" Residue "B TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 561": "OD1" <-> "OD2" Residue "B ASP 565": "OD1" <-> "OD2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B TYR 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 620": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 622": "NH1" <-> "NH2" Residue "B TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9485 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4759 Classifications: {'peptide': 597} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 574} Chain breaks: 1 Chain: "B" Number of atoms: 4695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4695 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 20, 'TRANS': 568} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.58 Number of scatterers: 9485 At special positions: 0 Unit cell: (77.19, 105.41, 140.27, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 43 16.00 P 3 15.00 O 1695 8.00 N 1670 7.00 C 6074 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: 3.61 Conformation dependent library (CDL) restraints added in 1.7 seconds 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 2 sheets defined 56.7% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 97 through 100 No H-bonds generated for 'chain 'A' and resid 97 through 100' Processing helix chain 'A' and resid 102 through 105 No H-bonds generated for 'chain 'A' and resid 102 through 105' Processing helix chain 'A' and resid 111 through 123 Processing helix chain 'A' and resid 127 through 135 Processing helix chain 'A' and resid 142 through 149 removed outlier: 3.934A pdb=" N VAL A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 174 removed outlier: 3.873A pdb=" N LEU A 158 " --> pdb=" O LEU A 154 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG A 165 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 No H-bonds generated for 'chain 'A' and resid 182 through 185' Processing helix chain 'A' and resid 201 through 236 Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 243 through 251 removed outlier: 4.262A pdb=" N GLY A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU A 249 " --> pdb=" O ALA A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 293 Proline residue: A 263 - end of helix removed outlier: 4.299A pdb=" N LEU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N GLU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 334 removed outlier: 3.505A pdb=" N ASP A 312 " --> pdb=" O ARG A 308 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU A 313 " --> pdb=" O SER A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 352 through 355 No H-bonds generated for 'chain 'A' and resid 352 through 355' Processing helix chain 'A' and resid 363 through 370 removed outlier: 4.012A pdb=" N LYS A 367 " --> pdb=" O GLU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 387 No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 412 through 431 removed outlier: 4.076A pdb=" N GLU A 427 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN A 430 " --> pdb=" O PHE A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 520 Processing helix chain 'A' and resid 553 through 556 No H-bonds generated for 'chain 'A' and resid 553 through 556' Processing helix chain 'A' and resid 563 through 568 removed outlier: 3.735A pdb=" N ARG A 568 " --> pdb=" O GLU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 583 Processing helix chain 'A' and resid 586 through 591 Processing helix chain 'A' and resid 601 through 604 No H-bonds generated for 'chain 'A' and resid 601 through 604' Processing helix chain 'A' and resid 607 through 620 removed outlier: 3.837A pdb=" N GLN A 611 " --> pdb=" O GLY A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 650 removed outlier: 3.967A pdb=" N LYS A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 666 removed outlier: 5.562A pdb=" N LYS A 665 " --> pdb=" O SER A 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 80 Processing helix chain 'B' and resid 99 through 108 removed outlier: 4.430A pdb=" N ARG B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU B 107 " --> pdb=" O SER B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 124 Processing helix chain 'B' and resid 127 through 136 Processing helix chain 'B' and resid 142 through 172 removed outlier: 4.051A pdb=" N VAL B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG B 152 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU B 155 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 158 " --> pdb=" O LEU B 154 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ALA B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 185 Processing helix chain 'B' and resid 196 through 235 Proline residue: B 218 - end of helix Processing helix chain 'B' and resid 239 through 288 Proline residue: B 243 - end of helix removed outlier: 4.001A pdb=" N ILE B 246 " --> pdb=" O TRP B 242 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 252 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR B 254 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE B 261 " --> pdb=" O VAL B 257 " (cutoff:3.500A) Proline residue: B 263 - end of helix Processing helix chain 'B' and resid 290 through 297 removed outlier: 3.526A pdb=" N PHE B 295 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N TYR B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY B 297 " --> pdb=" O ILE B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 346 removed outlier: 3.864A pdb=" N LEU B 305 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 306 " --> pdb=" O GLU B 302 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N TRP B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N VAL B 338 " --> pdb=" O LEU B 334 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TRP B 339 " --> pdb=" O MET B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 removed outlier: 5.000A pdb=" N THR B 355 " --> pdb=" O ILE B 351 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 356 " --> pdb=" O ILE B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.668A pdb=" N ALA B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 431 removed outlier: 3.502A pdb=" N THR B 410 " --> pdb=" O TYR B 406 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY B 414 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N TYR B 415 " --> pdb=" O GLU B 411 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 417 " --> pdb=" O ALA B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 511 No H-bonds generated for 'chain 'B' and resid 509 through 511' Processing helix chain 'B' and resid 513 through 520 removed outlier: 4.180A pdb=" N PHE B 517 " --> pdb=" O LYS B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 557 No H-bonds generated for 'chain 'B' and resid 554 through 557' Processing helix chain 'B' and resid 573 through 583 Processing helix chain 'B' and resid 586 through 591 Processing helix chain 'B' and resid 601 through 604 No H-bonds generated for 'chain 'B' and resid 601 through 604' Processing helix chain 'B' and resid 607 through 620 Processing helix chain 'B' and resid 638 through 650 removed outlier: 3.991A pdb=" N LYS B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA B 650 " --> pdb=" O ALA B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 663 No H-bonds generated for 'chain 'B' and resid 661 through 663' Processing sheet with id= A, first strand: chain 'A' and resid 466 through 469 removed outlier: 5.433A pdb=" N LEU A 493 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 467 through 470 removed outlier: 6.664A pdb=" N LEU B 531 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL B 470 " --> pdb=" O LEU B 531 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LYS B 533 " --> pdb=" O VAL B 470 " (cutoff:3.500A) 431 hydrogen bonds defined for protein. 1275 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1508 1.31 - 1.44: 2649 1.44 - 1.57: 5457 1.57 - 1.70: 7 1.70 - 1.82: 72 Bond restraints: 9693 Sorted by residual: bond pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " ideal model delta sigma weight residual 1.526 1.323 0.203 1.10e-02 8.26e+03 3.40e+02 bond pdb=" C1' ATP A 801 " pdb=" C2' ATP A 801 " ideal model delta sigma weight residual 1.531 1.365 0.166 1.20e-02 6.94e+03 1.92e+02 bond pdb=" C4' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.444 1.596 -0.152 1.10e-02 8.26e+03 1.92e+02 bond pdb=" C6 ATP A 801 " pdb=" N6 ATP A 801 " ideal model delta sigma weight residual 1.337 1.446 -0.109 1.10e-02 8.26e+03 9.89e+01 bond pdb=" C1' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.416 1.536 -0.120 1.30e-02 5.92e+03 8.59e+01 ... (remaining 9688 not shown) Histogram of bond angle deviations from ideal: 98.76 - 106.18: 238 106.18 - 113.59: 5041 113.59 - 121.00: 4938 121.00 - 128.41: 2836 128.41 - 135.82: 81 Bond angle restraints: 13134 Sorted by residual: angle pdb=" PA ATP A 801 " pdb=" O3A ATP A 801 " pdb=" PB ATP A 801 " ideal model delta sigma weight residual 136.83 117.82 19.01 1.00e+00 1.00e+00 3.61e+02 angle pdb=" PB ATP A 801 " pdb=" O3B ATP A 801 " pdb=" PG ATP A 801 " ideal model delta sigma weight residual 139.87 123.62 16.25 1.00e+00 1.00e+00 2.64e+02 angle pdb=" C5 ATP A 801 " pdb=" C4 ATP A 801 " pdb=" N3 ATP A 801 " ideal model delta sigma weight residual 126.80 118.03 8.77 1.00e+00 1.00e+00 7.69e+01 angle pdb=" N ILE A 402 " pdb=" CA ILE A 402 " pdb=" C ILE A 402 " ideal model delta sigma weight residual 112.29 104.35 7.94 9.40e-01 1.13e+00 7.14e+01 angle pdb=" N SER B 562 " pdb=" CA SER B 562 " pdb=" C SER B 562 " ideal model delta sigma weight residual 111.07 119.57 -8.50 1.07e+00 8.73e-01 6.31e+01 ... (remaining 13129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5017 17.18 - 34.36: 612 34.36 - 51.54: 125 51.54 - 68.73: 37 68.73 - 85.91: 18 Dihedral angle restraints: 5809 sinusoidal: 2359 harmonic: 3450 Sorted by residual: dihedral pdb=" CA MET B 186 " pdb=" C MET B 186 " pdb=" N ASP B 187 " pdb=" CA ASP B 187 " ideal model delta harmonic sigma weight residual -180.00 -103.58 -76.42 0 5.00e+00 4.00e-02 2.34e+02 dihedral pdb=" CA ASP A 361 " pdb=" C ASP A 361 " pdb=" N ALA A 362 " pdb=" CA ALA A 362 " ideal model delta harmonic sigma weight residual 0.00 30.86 -30.86 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA ASP B 194 " pdb=" C ASP B 194 " pdb=" N GLN B 195 " pdb=" CA GLN B 195 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 ... (remaining 5806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 1019 0.092 - 0.184: 373 0.184 - 0.277: 62 0.277 - 0.369: 9 0.369 - 0.461: 2 Chirality restraints: 1465 Sorted by residual: chirality pdb=" CA PHE A 295 " pdb=" N PHE A 295 " pdb=" C PHE A 295 " pdb=" CB PHE A 295 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA GLN B 177 " pdb=" N GLN B 177 " pdb=" C GLN B 177 " pdb=" CB GLN B 177 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.76e+00 chirality pdb=" CA LEU A 160 " pdb=" N LEU A 160 " pdb=" C LEU A 160 " pdb=" CB LEU A 160 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1462 not shown) Planarity restraints: 1662 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 218 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C PRO B 218 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO B 218 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU B 219 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 181 " -0.035 2.00e-02 2.50e+03 2.18e-02 9.54e+00 pdb=" CG TYR B 181 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR B 181 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 181 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR B 181 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 181 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR B 181 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 181 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 186 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.11e+00 pdb=" C MET B 186 " -0.049 2.00e-02 2.50e+03 pdb=" O MET B 186 " 0.019 2.00e-02 2.50e+03 pdb=" N ASP B 187 " 0.016 2.00e-02 2.50e+03 ... (remaining 1659 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 338 2.70 - 3.25: 9622 3.25 - 3.80: 14930 3.80 - 4.35: 20028 4.35 - 4.90: 31815 Nonbonded interactions: 76733 Sorted by model distance: nonbonded pdb=" O ASN A 509 " pdb=" O3B ATP A 801 " model vdw 2.153 3.040 nonbonded pdb=" O VAL B 482 " pdb=" OH TYR B 527 " model vdw 2.356 2.440 nonbonded pdb=" O LEU B 520 " pdb=" OH TYR B 541 " model vdw 2.371 2.440 nonbonded pdb=" N PHE B 295 " pdb=" O PHE B 295 " model vdw 2.373 2.496 nonbonded pdb=" O SER B 103 " pdb=" OG SER B 103 " model vdw 2.376 2.440 ... (remaining 76728 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 68 through 436 or resid 461 through 680)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.650 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: 0.000 Extract box with map and model: 11.660 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.010 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 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 : 0.009 0.203 9693 Z= 0.563 Angle : 1.426 19.006 13134 Z= 0.990 Chirality : 0.094 0.461 1465 Planarity : 0.007 0.032 1662 Dihedral : 16.443 85.906 3591 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.59 % Favored : 90.15 % Rotamer: Outliers : 3.51 % Allowed : 7.83 % Favored : 88.65 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -4.80 (0.20), residues: 1178 helix: -2.71 (0.15), residues: 765 sheet: -3.13 (0.63), residues: 39 loop : -3.88 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP B 339 HIS 0.014 0.003 HIS A 669 PHE 0.023 0.004 PHE A 295 TYR 0.043 0.005 TYR B 181 ARG 0.010 0.001 ARG B 401 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6196 (ttt180) cc_final: 0.5849 (ttp-170) REVERT: A 281 TYR cc_start: 0.5604 (OUTLIER) cc_final: 0.5347 (t80) REVERT: A 406 TYR cc_start: 0.7421 (t80) cc_final: 0.7214 (m-80) REVERT: A 537 GLN cc_start: 0.8228 (pt0) cc_final: 0.8026 (pm20) REVERT: A 566 MET cc_start: 0.8254 (tmm) cc_final: 0.7502 (ttt) REVERT: B 250 VAL cc_start: 0.7814 (t) cc_final: 0.7483 (m) REVERT: B 278 GLU cc_start: 0.6904 (tt0) cc_final: 0.6652 (tt0) REVERT: B 321 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7382 (mt) REVERT: B 322 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8037 (tt) REVERT: B 329 MET cc_start: 0.8007 (ttp) cc_final: 0.7595 (ttt) REVERT: B 539 MET cc_start: 0.5583 (mtp) cc_final: 0.5358 (mtp) REVERT: B 561 ASP cc_start: 0.5338 (OUTLIER) cc_final: 0.4833 (m-30) REVERT: B 610 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6632 (mmtt) REVERT: B 680 LYS cc_start: 0.5097 (OUTLIER) cc_final: 0.4599 (mtmm) outliers start: 35 outliers final: 7 residues processed: 152 average time/residue: 0.2626 time to fit residues: 54.3855 Evaluate side-chains 113 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 662 SER Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 680 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 106 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: A 472 GLN A 621 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9693 Z= 0.244 Angle : 0.700 9.196 13134 Z= 0.368 Chirality : 0.043 0.173 1465 Planarity : 0.005 0.043 1662 Dihedral : 10.156 78.401 1390 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer: Outliers : 2.71 % Allowed : 11.35 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -3.06 (0.22), residues: 1178 helix: -1.37 (0.18), residues: 771 sheet: -3.10 (0.67), residues: 32 loop : -3.10 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 326 HIS 0.006 0.001 HIS A 97 PHE 0.015 0.002 PHE A 295 TYR 0.019 0.002 TYR B 357 ARG 0.008 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 106 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6189 (ttt180) cc_final: 0.5843 (ttp-170) REVERT: A 281 TYR cc_start: 0.5813 (OUTLIER) cc_final: 0.5515 (t80) REVERT: A 324 ARG cc_start: 0.6761 (tpp80) cc_final: 0.5959 (ptm160) REVERT: A 406 TYR cc_start: 0.7453 (t80) cc_final: 0.6893 (m-80) REVERT: A 537 GLN cc_start: 0.8253 (pt0) cc_final: 0.7974 (pm20) REVERT: A 566 MET cc_start: 0.8410 (tmm) cc_final: 0.8099 (tmm) REVERT: B 96 LEU cc_start: 0.8079 (tp) cc_final: 0.7869 (tt) REVERT: B 278 GLU cc_start: 0.7027 (tt0) cc_final: 0.6761 (tt0) REVERT: B 321 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7149 (mt) REVERT: B 539 MET cc_start: 0.5734 (mtp) cc_final: 0.5348 (mtp) REVERT: B 610 LYS cc_start: 0.7397 (OUTLIER) cc_final: 0.6629 (mmtp) REVERT: B 648 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7901 (pttm) outliers start: 27 outliers final: 8 residues processed: 128 average time/residue: 0.2503 time to fit residues: 43.5281 Evaluate side-chains 109 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 610 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 106 optimal weight: 8.9990 chunk 114 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 36 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN B 430 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9693 Z= 0.252 Angle : 0.638 8.666 13134 Z= 0.331 Chirality : 0.042 0.149 1465 Planarity : 0.004 0.048 1662 Dihedral : 9.034 75.286 1373 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.21 % Allowed : 12.85 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.23 (0.24), residues: 1178 helix: -0.71 (0.19), residues: 763 sheet: -2.52 (0.72), residues: 32 loop : -2.84 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 326 HIS 0.005 0.001 HIS A 621 PHE 0.012 0.001 PHE B 265 TYR 0.019 0.002 TYR B 357 ARG 0.006 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 108 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7799 (mmm) cc_final: 0.7523 (mmt) REVERT: A 234 ARG cc_start: 0.6136 (ttt180) cc_final: 0.5736 (ttp-170) REVERT: A 281 TYR cc_start: 0.5881 (OUTLIER) cc_final: 0.5612 (t80) REVERT: A 324 ARG cc_start: 0.6781 (tpp80) cc_final: 0.5965 (ptm160) REVERT: A 501 MET cc_start: 0.8020 (mmm) cc_final: 0.7715 (mmm) REVERT: A 537 GLN cc_start: 0.8269 (pt0) cc_final: 0.7979 (pm20) REVERT: A 566 MET cc_start: 0.8410 (tmm) cc_final: 0.8129 (tmm) REVERT: B 539 MET cc_start: 0.5604 (mtp) cc_final: 0.5164 (mtp) REVERT: B 548 MET cc_start: 0.5170 (mmp) cc_final: 0.4173 (tpp) REVERT: B 610 LYS cc_start: 0.7402 (OUTLIER) cc_final: 0.6773 (mmtp) REVERT: B 621 HIS cc_start: 0.6324 (m-70) cc_final: 0.5705 (m170) outliers start: 32 outliers final: 18 residues processed: 133 average time/residue: 0.2406 time to fit residues: 44.0827 Evaluate side-chains 117 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 97 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 649 ASP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 610 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 11 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 chunk 101 optimal weight: 10.0000 chunk 30 optimal weight: 0.3980 chunk 94 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9693 Z= 0.269 Angle : 0.633 9.937 13134 Z= 0.324 Chirality : 0.042 0.226 1465 Planarity : 0.004 0.052 1662 Dihedral : 8.631 79.218 1371 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.21 % Allowed : 16.67 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1178 helix: -0.40 (0.19), residues: 760 sheet: -2.07 (0.82), residues: 32 loop : -2.72 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.005 0.001 HIS A 97 PHE 0.012 0.001 PHE B 265 TYR 0.024 0.002 TYR A 406 ARG 0.007 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 102 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 67 MET cc_start: 0.7734 (mmm) cc_final: 0.7487 (mmt) REVERT: A 155 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: A 234 ARG cc_start: 0.6178 (ttt180) cc_final: 0.5740 (ttp-170) REVERT: A 407 LYS cc_start: 0.8512 (tmtt) cc_final: 0.8311 (tttm) REVERT: A 537 GLN cc_start: 0.8242 (pt0) cc_final: 0.7955 (pm20) REVERT: A 566 MET cc_start: 0.8413 (tmm) cc_final: 0.8131 (tmm) REVERT: A 622 ARG cc_start: 0.8366 (mtm-85) cc_final: 0.8100 (mtt-85) REVERT: B 539 MET cc_start: 0.5471 (mtp) cc_final: 0.5056 (mtp) REVERT: B 610 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6406 (mmtp) outliers start: 32 outliers final: 18 residues processed: 125 average time/residue: 0.2422 time to fit residues: 41.4583 Evaluate side-chains 118 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 610 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 84 optimal weight: 0.0980 chunk 46 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 28 optimal weight: 0.8980 chunk 38 optimal weight: 10.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN B 433 HIS B 621 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9693 Z= 0.224 Angle : 0.581 8.135 13134 Z= 0.299 Chirality : 0.040 0.138 1465 Planarity : 0.004 0.053 1662 Dihedral : 8.206 88.284 1366 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 3.11 % Allowed : 17.27 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.48 (0.25), residues: 1178 helix: -0.12 (0.19), residues: 766 sheet: -1.81 (0.85), residues: 32 loop : -2.63 (0.29), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 595 HIS 0.003 0.001 HIS A 621 PHE 0.011 0.001 PHE B 265 TYR 0.018 0.001 TYR B 310 ARG 0.007 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6165 (ttt180) cc_final: 0.5710 (ttp-170) REVERT: A 537 GLN cc_start: 0.8259 (pt0) cc_final: 0.7954 (pm20) REVERT: A 566 MET cc_start: 0.8429 (tmm) cc_final: 0.8170 (tmm) REVERT: A 622 ARG cc_start: 0.8314 (mtm-85) cc_final: 0.8056 (mtt-85) REVERT: B 539 MET cc_start: 0.5481 (mtp) cc_final: 0.5040 (mtp) outliers start: 31 outliers final: 17 residues processed: 125 average time/residue: 0.2452 time to fit residues: 41.8207 Evaluate side-chains 113 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 610 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 9.9990 chunk 22 optimal weight: 0.0040 chunk 66 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 37 optimal weight: 0.0470 chunk 59 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 overall best weight: 0.3890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9693 Z= 0.178 Angle : 0.564 9.109 13134 Z= 0.286 Chirality : 0.040 0.260 1465 Planarity : 0.004 0.055 1662 Dihedral : 7.758 83.747 1366 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.41 % Allowed : 17.47 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.15 (0.25), residues: 1178 helix: 0.13 (0.20), residues: 766 sheet: -0.68 (1.13), residues: 22 loop : -2.56 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 595 HIS 0.004 0.001 HIS B 420 PHE 0.010 0.001 PHE B 265 TYR 0.018 0.001 TYR B 310 ARG 0.006 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 104 time to evaluate : 1.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6159 (ttt180) cc_final: 0.5690 (ttp-170) REVERT: A 537 GLN cc_start: 0.8258 (pt0) cc_final: 0.7932 (pm20) REVERT: A 566 MET cc_start: 0.8408 (tmm) cc_final: 0.8111 (tmm) REVERT: A 622 ARG cc_start: 0.8290 (mtm-85) cc_final: 0.7953 (mtt-85) REVERT: B 321 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7161 (mt) REVERT: B 539 MET cc_start: 0.5630 (mtp) cc_final: 0.5136 (mtp) REVERT: B 610 LYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6292 (mmtp) outliers start: 34 outliers final: 16 residues processed: 128 average time/residue: 0.2422 time to fit residues: 42.6556 Evaluate side-chains 109 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 320 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 610 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 63 optimal weight: 0.5980 chunk 112 optimal weight: 30.0000 chunk 70 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 45 optimal weight: 0.0270 overall best weight: 0.8842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9693 Z= 0.262 Angle : 0.602 10.283 13134 Z= 0.304 Chirality : 0.042 0.222 1465 Planarity : 0.004 0.054 1662 Dihedral : 7.803 86.099 1366 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.11 % Allowed : 18.47 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.21 (0.25), residues: 1178 helix: 0.10 (0.19), residues: 764 sheet: -1.50 (0.89), residues: 32 loop : -2.55 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 595 HIS 0.007 0.001 HIS B 420 PHE 0.012 0.001 PHE B 265 TYR 0.017 0.001 TYR B 357 ARG 0.006 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7295 (pt0) REVERT: A 234 ARG cc_start: 0.6213 (ttt180) cc_final: 0.5702 (ttp-170) REVERT: A 537 GLN cc_start: 0.8278 (pt0) cc_final: 0.7951 (pm20) REVERT: A 566 MET cc_start: 0.8407 (tmm) cc_final: 0.8142 (tmm) REVERT: B 321 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7250 (mt) REVERT: B 539 MET cc_start: 0.5588 (mtp) cc_final: 0.5100 (mtp) REVERT: B 648 LYS cc_start: 0.7970 (pttm) cc_final: 0.7658 (mmtt) outliers start: 21 outliers final: 18 residues processed: 117 average time/residue: 0.2325 time to fit residues: 38.0227 Evaluate side-chains 116 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 88 optimal weight: 5.9990 chunk 102 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 621 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9693 Z= 0.218 Angle : 0.581 8.786 13134 Z= 0.292 Chirality : 0.041 0.211 1465 Planarity : 0.004 0.060 1662 Dihedral : 7.367 80.553 1362 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.91 % Allowed : 18.67 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.04 (0.25), residues: 1178 helix: 0.23 (0.20), residues: 767 sheet: -0.63 (1.14), residues: 22 loop : -2.53 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 595 HIS 0.007 0.001 HIS B 420 PHE 0.011 0.001 PHE B 265 TYR 0.018 0.001 TYR B 310 ARG 0.006 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6238 (ttt180) cc_final: 0.5699 (ttp-170) REVERT: A 478 ASN cc_start: 0.8175 (t0) cc_final: 0.7863 (t0) REVERT: A 537 GLN cc_start: 0.8263 (pt0) cc_final: 0.7942 (pm20) REVERT: A 566 MET cc_start: 0.8419 (tmm) cc_final: 0.8191 (tmm) REVERT: B 539 MET cc_start: 0.5554 (mtp) cc_final: 0.5079 (mtp) REVERT: B 648 LYS cc_start: 0.8063 (pttm) cc_final: 0.7745 (mmtt) outliers start: 19 outliers final: 18 residues processed: 110 average time/residue: 0.2493 time to fit residues: 38.0711 Evaluate side-chains 111 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 93 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 292 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 550 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 108 optimal weight: 9.9990 chunk 63 optimal weight: 0.6980 chunk 45 optimal weight: 0.0000 chunk 82 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9693 Z= 0.276 Angle : 0.610 11.635 13134 Z= 0.304 Chirality : 0.042 0.200 1465 Planarity : 0.004 0.054 1662 Dihedral : 7.416 82.947 1362 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.41 % Allowed : 18.88 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.16 (0.25), residues: 1178 helix: 0.12 (0.19), residues: 778 sheet: -0.71 (1.12), residues: 22 loop : -2.61 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 595 HIS 0.005 0.001 HIS B 97 PHE 0.012 0.001 PHE B 265 TYR 0.018 0.001 TYR B 310 ARG 0.006 0.000 ARG A 568 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 97 time to evaluate : 2.652 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7686 (OUTLIER) cc_final: 0.7305 (pt0) REVERT: A 234 ARG cc_start: 0.6254 (ttt180) cc_final: 0.5769 (ttp-170) REVERT: A 537 GLN cc_start: 0.8256 (pt0) cc_final: 0.7935 (pm20) REVERT: A 566 MET cc_start: 0.8412 (tmm) cc_final: 0.8140 (tmm) REVERT: B 321 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7245 (mt) REVERT: B 539 MET cc_start: 0.5584 (mtp) cc_final: 0.5112 (mtp) REVERT: B 610 LYS cc_start: 0.7261 (OUTLIER) cc_final: 0.6263 (mmtp) REVERT: B 648 LYS cc_start: 0.8056 (pttm) cc_final: 0.7734 (mmtt) outliers start: 24 outliers final: 18 residues processed: 116 average time/residue: 0.2481 time to fit residues: 39.6480 Evaluate side-chains 116 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 610 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 20.0000 chunk 67 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 116 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 0.0770 chunk 73 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9693 Z= 0.195 Angle : 0.584 12.664 13134 Z= 0.289 Chirality : 0.040 0.185 1465 Planarity : 0.004 0.054 1662 Dihedral : 7.025 74.512 1359 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.11 % Allowed : 19.68 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.01 (0.25), residues: 1178 helix: 0.29 (0.20), residues: 773 sheet: -0.59 (1.13), residues: 22 loop : -2.66 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 326 HIS 0.005 0.001 HIS B 420 PHE 0.011 0.001 PHE B 540 TYR 0.018 0.001 TYR B 310 ARG 0.007 0.000 ARG A 568 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2356 Ramachandran restraints generated. 1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.066 Fit side-chains revert: symmetry clash REVERT: A 234 ARG cc_start: 0.6246 (ttt180) cc_final: 0.5755 (ttp-170) REVERT: A 478 ASN cc_start: 0.8136 (t0) cc_final: 0.7836 (t0) REVERT: A 501 MET cc_start: 0.8003 (mmm) cc_final: 0.7787 (mmm) REVERT: A 537 GLN cc_start: 0.8257 (pt0) cc_final: 0.7936 (pm20) REVERT: A 566 MET cc_start: 0.8420 (tmm) cc_final: 0.8189 (tmm) REVERT: A 568 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7872 (ttp80) REVERT: B 321 LEU cc_start: 0.7480 (OUTLIER) cc_final: 0.7197 (mt) REVERT: B 346 MET cc_start: 0.7310 (ttm) cc_final: 0.7058 (ttt) REVERT: B 539 MET cc_start: 0.5499 (mtp) cc_final: 0.5046 (mtp) REVERT: B 610 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6308 (mmtp) REVERT: B 648 LYS cc_start: 0.8002 (pttm) cc_final: 0.7713 (mmtt) outliers start: 21 outliers final: 18 residues processed: 112 average time/residue: 0.2414 time to fit residues: 37.5851 Evaluate side-chains 113 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 155 GLU Chi-restraints excluded: chain A residue 271 GLU Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 595 TRP Chi-restraints excluded: chain A residue 679 TRP Chi-restraints excluded: chain B residue 140 ILE Chi-restraints excluded: chain B residue 149 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 483 THR Chi-restraints excluded: chain B residue 502 HIS Chi-restraints excluded: chain B residue 550 VAL Chi-restraints excluded: chain B residue 610 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 8.9990 chunk 28 optimal weight: 0.0980 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 GLN ** A 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4593 r_free = 0.4593 target = 0.241623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 153)---------------| | r_work = 0.3967 r_free = 0.3967 target = 0.168376 restraints weight = 9290.094| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.67 r_work: 0.3523 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9693 Z= 0.207 Angle : 0.587 11.641 13134 Z= 0.289 Chirality : 0.041 0.188 1465 Planarity : 0.004 0.054 1662 Dihedral : 6.905 71.682 1359 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.41 % Allowed : 19.68 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.25), residues: 1178 helix: 0.34 (0.19), residues: 777 sheet: -0.53 (1.16), residues: 22 loop : -2.57 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 595 HIS 0.005 0.001 HIS B 420 PHE 0.011 0.001 PHE B 265 TYR 0.018 0.001 TYR B 310 ARG 0.006 0.000 ARG A 568 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.94 seconds wall clock time: 44 minutes 41.86 seconds (2681.86 seconds total)