Starting phenix.real_space_refine on Tue Apr 9 20:42:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk5_22362/04_2024/7jk5_22362_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk5_22362/04_2024/7jk5_22362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk5_22362/04_2024/7jk5_22362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk5_22362/04_2024/7jk5_22362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk5_22362/04_2024/7jk5_22362_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jk5_22362/04_2024/7jk5_22362_updated.pdb" } resolution = 3.9 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= 0.001 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 73 5.49 5 Mg 3 5.21 5 S 89 5.16 5 C 10879 2.51 5 N 3040 2.21 5 O 3324 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 421": "OE1" <-> "OE2" Residue "C ARG 20": "NH1" <-> "NH2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ARG 89": "NH1" <-> "NH2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C GLU 159": "OE1" <-> "OE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C GLU 443": "OE1" <-> "OE2" Residue "C GLU 477": "OE1" <-> "OE2" Residue "C GLU 496": "OE1" <-> "OE2" Residue "C GLU 592": "OE1" <-> "OE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 45": "OE1" <-> "OE2" Residue "D GLU 236": "OE1" <-> "OE2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D GLU 389": "OE1" <-> "OE2" Residue "E GLU 9": "OE1" <-> "OE2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E GLU 106": "OE1" <-> "OE2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 164": "OE1" <-> "OE2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E ARG 293": "NH1" <-> "NH2" Residue "E GLU 320": "OE1" <-> "OE2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E GLU 395": "OE1" <-> "OE2" Residue "E GLU 427": "OE1" <-> "OE2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A ARG 676": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 725": "NH1" <-> "NH2" Residue "A ARG 785": "NH1" <-> "NH2" Residue "A ARG 880": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 17408 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1407 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "C" Number of atoms: 4747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4747 Classifications: {'peptide': 590} Link IDs: {'PTRANS': 22, 'TRANS': 567} Chain breaks: 8 Chain: "D" Number of atoms: 3549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3549 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 11, 'TRANS': 429} Chain breaks: 2 Chain: "E" Number of atoms: 3127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 3127 Classifications: {'peptide': 393} Link IDs: {'PTRANS': 11, 'TRANS': 381} Chain breaks: 4 Chain: "F" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 120 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "A" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3050 Classifications: {'peptide': 390} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 372} Chain breaks: 1 Chain: "H" Number of atoms: 652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 652 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "I" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 660 Classifications: {'DNA': 32} Link IDs: {'rna3p': 31} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.35, per 1000 atoms: 0.54 Number of scatterers: 17408 At special positions: 0 Unit cell: (122.12, 155.66, 109.22, 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 89 16.00 P 73 15.00 Mg 3 11.99 O 3324 8.00 N 3040 7.00 C 10879 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.82 Conformation dependent library (CDL) restraints added in 2.9 seconds 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3834 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 11 sheets defined 56.7% alpha, 6.0% beta 32 base pairs and 57 stacking pairs defined. Time for finding SS restraints: 7.89 Creating SS restraints... Processing helix chain 'B' and resid 329 through 349 removed outlier: 3.684A pdb=" N TYR B 339 " --> pdb=" O GLU B 335 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N PHE B 340 " --> pdb=" O TYR B 336 " (cutoff:3.500A) Proline residue: B 341 - end of helix removed outlier: 3.677A pdb=" N GLU B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 371 Processing helix chain 'B' and resid 390 through 399 Processing helix chain 'B' and resid 411 through 423 Processing helix chain 'B' and resid 445 through 455 Processing helix chain 'B' and resid 471 through 473 No H-bonds generated for 'chain 'B' and resid 471 through 473' Processing helix chain 'B' and resid 477 through 482 Processing helix chain 'B' and resid 498 through 501 No H-bonds generated for 'chain 'B' and resid 498 through 501' Processing helix chain 'C' and resid 42 through 45 No H-bonds generated for 'chain 'C' and resid 42 through 45' Processing helix chain 'C' and resid 48 through 87 removed outlier: 4.701A pdb=" N ARG C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N THR C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 123 removed outlier: 4.295A pdb=" N SER C 112 " --> pdb=" O PRO C 108 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN C 113 " --> pdb=" O ASP C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 140 through 158 Processing helix chain 'C' and resid 185 through 195 Processing helix chain 'C' and resid 217 through 230 Processing helix chain 'C' and resid 246 through 252 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 271 through 281 Processing helix chain 'C' and resid 294 through 306 Processing helix chain 'C' and resid 311 through 328 removed outlier: 4.830A pdb=" N GLY C 328 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 334 Processing helix chain 'C' and resid 338 through 347 Processing helix chain 'C' and resid 351 through 357 Processing helix chain 'C' and resid 360 through 367 Proline residue: C 364 - end of helix Processing helix chain 'C' and resid 376 through 380 removed outlier: 3.520A pdb=" N THR C 380 " --> pdb=" O ILE C 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 376 through 380' Processing helix chain 'C' and resid 383 through 415 Proline residue: C 390 - end of helix Processing helix chain 'C' and resid 426 through 435 Processing helix chain 'C' and resid 438 through 440 No H-bonds generated for 'chain 'C' and resid 438 through 440' Processing helix chain 'C' and resid 442 through 452 Processing helix chain 'C' and resid 456 through 476 Processing helix chain 'C' and resid 485 through 506 Proline residue: C 493 - end of helix Processing helix chain 'C' and resid 564 through 575 Processing helix chain 'C' and resid 600 through 606 Processing helix chain 'C' and resid 610 through 619 Processing helix chain 'C' and resid 621 through 625 Processing helix chain 'C' and resid 644 through 654 removed outlier: 4.035A pdb=" N VAL C 648 " --> pdb=" O ASP C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 671 Processing helix chain 'C' and resid 688 through 702 Processing helix chain 'D' and resid 3 through 20 Processing helix chain 'D' and resid 30 through 45 removed outlier: 3.552A pdb=" N SER D 34 " --> pdb=" O ALA D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 Proline residue: D 75 - end of helix Processing helix chain 'D' and resid 79 through 82 No H-bonds generated for 'chain 'D' and resid 79 through 82' Processing helix chain 'D' and resid 96 through 106 Processing helix chain 'D' and resid 121 through 134 removed outlier: 3.505A pdb=" N ALA D 134 " --> pdb=" O GLN D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 156 through 166 removed outlier: 5.927A pdb=" N LEU D 160 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N PHE D 165 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 212 through 223 removed outlier: 3.501A pdb=" N LEU D 223 " --> pdb=" O CYS D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 242 Processing helix chain 'D' and resid 258 through 260 No H-bonds generated for 'chain 'D' and resid 258 through 260' Processing helix chain 'D' and resid 265 through 280 Processing helix chain 'D' and resid 282 through 294 Processing helix chain 'D' and resid 298 through 311 removed outlier: 4.377A pdb=" N HIS D 311 " --> pdb=" O ARG D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 316 No H-bonds generated for 'chain 'D' and resid 314 through 316' Processing helix chain 'D' and resid 321 through 332 Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.511A pdb=" N CYS D 341 " --> pdb=" O ILE D 337 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY D 342 " --> pdb=" O GLU D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 368 through 381 removed outlier: 3.971A pdb=" N PHE D 378 " --> pdb=" O ARG D 374 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS D 380 " --> pdb=" O SER D 376 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL D 381 " --> pdb=" O LYS D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 390 through 402 Processing helix chain 'D' and resid 433 through 442 removed outlier: 3.778A pdb=" N GLN D 441 " --> pdb=" O HIS D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 454 Processing helix chain 'E' and resid 2 through 9 Processing helix chain 'E' and resid 16 through 25 Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 71 through 73 No H-bonds generated for 'chain 'E' and resid 71 through 73' Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 101 through 109 Processing helix chain 'E' and resid 115 through 117 No H-bonds generated for 'chain 'E' and resid 115 through 117' Processing helix chain 'E' and resid 128 through 133 removed outlier: 4.053A pdb=" N ARG E 132 " --> pdb=" O GLU E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 143 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 163 through 166 Processing helix chain 'E' and resid 185 through 205 removed outlier: 4.117A pdb=" N ASP E 195 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N PHE E 196 " --> pdb=" O LEU E 192 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N GLN E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN E 198 " --> pdb=" O SER E 194 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU E 205 " --> pdb=" O ASN E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 220 removed outlier: 3.915A pdb=" N GLU E 219 " --> pdb=" O GLU E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 234 Processing helix chain 'E' and resid 237 through 239 No H-bonds generated for 'chain 'E' and resid 237 through 239' Processing helix chain 'E' and resid 244 through 258 removed outlier: 4.257A pdb=" N LYS E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 260 through 263 No H-bonds generated for 'chain 'E' and resid 260 through 263' Processing helix chain 'E' and resid 276 through 286 Proline residue: E 282 - end of helix removed outlier: 3.812A pdb=" N SER E 285 " --> pdb=" O GLY E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 323 through 335 Processing helix chain 'E' and resid 342 through 346 removed outlier: 3.957A pdb=" N LEU E 346 " --> pdb=" O ASP E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 393 Processing helix chain 'E' and resid 401 through 412 Processing helix chain 'E' and resid 422 through 424 No H-bonds generated for 'chain 'E' and resid 422 through 424' Processing helix chain 'E' and resid 438 through 447 Processing helix chain 'F' and resid 225 through 235 Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 551 through 559 Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'A' and resid 604 through 620 Processing helix chain 'A' and resid 634 through 636 No H-bonds generated for 'chain 'A' and resid 634 through 636' Processing helix chain 'A' and resid 640 through 650 removed outlier: 4.173A pdb=" N ILE A 647 " --> pdb=" O TYR A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 669 Processing helix chain 'A' and resid 686 through 689 Processing helix chain 'A' and resid 695 through 705 Proline residue: A 704 - end of helix Processing helix chain 'A' and resid 722 through 726 Processing helix chain 'A' and resid 747 through 757 removed outlier: 3.860A pdb=" N VAL A 754 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 783 through 799 Processing helix chain 'A' and resid 807 through 817 Processing helix chain 'A' and resid 822 through 827 Processing helix chain 'A' and resid 831 through 847 removed outlier: 3.521A pdb=" N ALA A 841 " --> pdb=" O LEU A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 868 Processing helix chain 'A' and resid 875 through 887 Processing helix chain 'A' and resid 910 through 917 removed outlier: 3.970A pdb=" N HIS A 914 " --> pdb=" O ALA A 910 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 352 through 355 removed outlier: 3.649A pdb=" N LEU B 354 " --> pdb=" O SER B 486 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 378 through 382 removed outlier: 7.226A pdb=" N PHE B 431 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N VAL B 381 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 433 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 96 through 101 Processing sheet with id= D, first strand: chain 'C' and resid 127 through 131 removed outlier: 6.022A pdb=" N GLN C 204 " --> pdb=" O MET C 128 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N CYS C 130 " --> pdb=" O GLN C 204 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL C 206 " --> pdb=" O CYS C 130 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL C 239 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 706 through 708 Processing sheet with id= F, first strand: chain 'D' and resid 50 through 55 removed outlier: 6.996A pdb=" N VAL D 142 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N LEU D 178 " --> pdb=" O VAL D 142 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N PHE D 144 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N VAL D 180 " --> pdb=" O PHE D 144 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU D 146 " --> pdb=" O VAL D 180 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 406 through 408 Processing sheet with id= H, first strand: chain 'E' and resid 176 through 180 removed outlier: 6.394A pdb=" N VAL E 155 " --> pdb=" O ILE E 37 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N LEU E 39 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU E 157 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N GLY E 41 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N SER E 159 " --> pdb=" O GLY E 41 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE E 123 " --> pdb=" O ILE E 156 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LEU E 158 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL E 125 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 416 through 420 removed outlier: 6.902A pdb=" N ARG E 431 " --> pdb=" O VAL E 419 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 592 through 597 removed outlier: 6.188A pdb=" N THR A 679 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N VAL A 714 " --> pdb=" O THR A 679 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU A 681 " --> pdb=" O VAL A 714 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE A 716 " --> pdb=" O LEU A 681 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL A 683 " --> pdb=" O ILE A 716 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLU A 628 " --> pdb=" O VAL A 680 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU A 682 " --> pdb=" O GLU A 628 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 630 " --> pdb=" O LEU A 682 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASP A 684 " --> pdb=" O LEU A 630 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE A 632 " --> pdb=" O ASP A 684 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 891 through 893 removed outlier: 3.514A pdb=" N ILE A 892 " --> pdb=" O LEU A 905 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 2076 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 72 hydrogen bonds 144 hydrogen bond angles 0 basepair planarities 32 basepair parallelities 57 stacking parallelities Total time for adding SS restraints: 6.81 Time building geometry restraints manager: 8.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4838 1.34 - 1.46: 3698 1.46 - 1.58: 9050 1.58 - 1.70: 141 1.70 - 1.82: 129 Bond restraints: 17856 Sorted by residual: bond pdb=" C4 ATP A1001 " pdb=" C5 ATP A1001 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.80e+01 bond pdb=" C4 ATP D 901 " pdb=" C5 ATP D 901 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.56e+01 bond pdb=" C4 ATP E 901 " pdb=" C5 ATP E 901 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.21e+01 bond pdb=" C5 ATP E 901 " pdb=" C6 ATP E 901 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.84e+01 bond pdb=" C5 ATP A1001 " pdb=" C6 ATP A1001 " ideal model delta sigma weight residual 1.409 1.464 -0.055 1.00e-02 1.00e+04 3.06e+01 ... (remaining 17851 not shown) Histogram of bond angle deviations from ideal: 96.72 - 104.56: 496 104.56 - 112.41: 9197 112.41 - 120.25: 8146 120.25 - 128.09: 6393 128.09 - 135.94: 193 Bond angle restraints: 24425 Sorted by residual: angle pdb=" PB ATP D 901 " pdb=" O3B ATP D 901 " pdb=" PG ATP D 901 " ideal model delta sigma weight residual 139.87 116.48 23.39 1.00e+00 1.00e+00 5.47e+02 angle pdb=" PB ATP E 901 " pdb=" O3B ATP E 901 " pdb=" PG ATP E 901 " ideal model delta sigma weight residual 139.87 118.21 21.66 1.00e+00 1.00e+00 4.69e+02 angle pdb=" PB ATP A1001 " pdb=" O3B ATP A1001 " pdb=" PG ATP A1001 " ideal model delta sigma weight residual 139.87 118.61 21.26 1.00e+00 1.00e+00 4.52e+02 angle pdb=" PA ATP D 901 " pdb=" O3A ATP D 901 " pdb=" PB ATP D 901 " ideal model delta sigma weight residual 136.83 115.70 21.13 1.00e+00 1.00e+00 4.46e+02 angle pdb=" PA ATP E 901 " pdb=" O3A ATP E 901 " pdb=" PB ATP E 901 " ideal model delta sigma weight residual 136.83 117.14 19.69 1.00e+00 1.00e+00 3.88e+02 ... (remaining 24420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 8961 17.81 - 35.62: 1190 35.62 - 53.43: 440 53.43 - 71.24: 129 71.24 - 89.05: 25 Dihedral angle restraints: 10745 sinusoidal: 4871 harmonic: 5874 Sorted by residual: dihedral pdb=" CA ALA E 136 " pdb=" C ALA E 136 " pdb=" N ASN E 137 " pdb=" CA ASN E 137 " ideal model delta harmonic sigma weight residual 180.00 151.03 28.97 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ASP C 337 " pdb=" C ASP C 337 " pdb=" N TYR C 338 " pdb=" CA TYR C 338 " ideal model delta harmonic sigma weight residual -180.00 -154.96 -25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLN D 158 " pdb=" C GLN D 158 " pdb=" N THR D 159 " pdb=" CA THR D 159 " ideal model delta harmonic sigma weight residual 180.00 -156.60 -23.40 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 10742 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1866 0.052 - 0.104: 751 0.104 - 0.155: 150 0.155 - 0.207: 35 0.207 - 0.259: 9 Chirality restraints: 2811 Sorted by residual: chirality pdb=" CA GLU E 9 " pdb=" N GLU E 9 " pdb=" C GLU E 9 " pdb=" CB GLU E 9 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ASN B 436 " pdb=" N ASN B 436 " pdb=" C ASN B 436 " pdb=" CB ASN B 436 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA ARG C 419 " pdb=" N ARG C 419 " pdb=" C ARG C 419 " pdb=" CB ARG C 419 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 2808 not shown) Planarity restraints: 2871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 485 " -0.030 2.00e-02 2.50e+03 2.42e-02 1.02e+01 pdb=" CG PHE B 485 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE B 485 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 485 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 485 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE B 485 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE B 485 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 237 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.08e+00 pdb=" C VAL C 237 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL C 237 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU C 238 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 639 " 0.047 5.00e-02 4.00e+02 7.09e-02 8.04e+00 pdb=" N PRO A 640 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 640 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 640 " 0.039 5.00e-02 4.00e+02 ... (remaining 2868 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 178 2.62 - 3.19: 14427 3.19 - 3.76: 28734 3.76 - 4.33: 37263 4.33 - 4.90: 58885 Nonbonded interactions: 139487 Sorted by model distance: nonbonded pdb=" O1G ATP D 901 " pdb="MG MG D 902 " model vdw 2.049 2.170 nonbonded pdb=" O2B ATP E 901 " pdb="MG MG E 902 " model vdw 2.067 2.170 nonbonded pdb=" OG1 THR A 605 " pdb="MG MG A1002 " model vdw 2.103 2.170 nonbonded pdb=" O3G ATP E 901 " pdb="MG MG E 902 " model vdw 2.104 2.170 nonbonded pdb=" O3G ATP A1001 " pdb="MG MG A1002 " model vdw 2.122 2.170 ... (remaining 139482 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.730 Check model and map are aligned: 0.260 Set scattering table: 0.180 Process input model: 54.230 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.080 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 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 : 0.007 0.076 17856 Z= 0.439 Angle : 1.118 23.391 24425 Z= 0.701 Chirality : 0.058 0.259 2811 Planarity : 0.007 0.071 2871 Dihedral : 19.285 89.048 6911 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.29 % Allowed : 6.00 % Favored : 93.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -3.05 (0.16), residues: 1961 helix: -2.63 (0.10), residues: 1180 sheet: -3.42 (0.32), residues: 156 loop : 0.32 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 191 HIS 0.009 0.002 HIS C 622 PHE 0.055 0.003 PHE B 485 TYR 0.030 0.003 TYR C 255 ARG 0.012 0.001 ARG E 213 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 300 time to evaluate : 2.071 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: B 335 GLU cc_start: 0.9321 (mm-30) cc_final: 0.9028 (mp0) REVERT: B 342 LYS cc_start: 0.9573 (tttm) cc_final: 0.9107 (ptpt) REVERT: B 343 TRP cc_start: 0.9286 (m-10) cc_final: 0.8896 (m100) REVERT: B 417 MET cc_start: 0.9126 (mmt) cc_final: 0.8745 (ptt) REVERT: B 421 GLU cc_start: 0.9079 (mt-10) cc_final: 0.8289 (mt-10) REVERT: B 474 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8598 (pp) REVERT: B 483 PHE cc_start: 0.8854 (OUTLIER) cc_final: 0.8534 (m-80) REVERT: B 493 MET cc_start: 0.7992 (mmt) cc_final: 0.7063 (tmm) REVERT: C 208 ILE cc_start: 0.9557 (mt) cc_final: 0.9323 (tp) REVERT: C 246 MET cc_start: 0.8117 (mmm) cc_final: 0.7916 (tpt) REVERT: C 323 MET cc_start: 0.9339 (tmm) cc_final: 0.9060 (tmm) REVERT: C 340 LYS cc_start: 0.9733 (tptp) cc_final: 0.9453 (tptm) REVERT: C 381 ASP cc_start: 0.9154 (t0) cc_final: 0.8940 (t0) REVERT: C 395 ASP cc_start: 0.9198 (t70) cc_final: 0.8816 (p0) REVERT: C 623 PHE cc_start: 0.9144 (t80) cc_final: 0.8697 (t80) REVERT: D 215 TYR cc_start: 0.8724 (t80) cc_final: 0.8491 (t80) REVERT: D 335 ASP cc_start: 0.9079 (m-30) cc_final: 0.8678 (p0) REVERT: D 341 CYS cc_start: 0.8910 (m) cc_final: 0.8659 (m) REVERT: D 346 LEU cc_start: 0.9418 (tp) cc_final: 0.9151 (tt) REVERT: D 421 GLN cc_start: 0.8783 (mt0) cc_final: 0.8093 (mp10) REVERT: D 426 MET cc_start: 0.9325 (mmm) cc_final: 0.9112 (mmm) REVERT: D 440 MET cc_start: 0.8961 (mmt) cc_final: 0.8679 (mmm) REVERT: E 69 LEU cc_start: 0.8989 (tp) cc_final: 0.7654 (tp) REVERT: E 80 MET cc_start: 0.9401 (ttm) cc_final: 0.9116 (tpp) REVERT: E 84 LEU cc_start: 0.9721 (mt) cc_final: 0.9519 (mt) REVERT: E 237 PHE cc_start: 0.8490 (m-10) cc_final: 0.8055 (m-10) REVERT: A 588 ASP cc_start: 0.8686 (m-30) cc_final: 0.8189 (p0) REVERT: A 790 CYS cc_start: 0.9594 (m) cc_final: 0.9366 (m) REVERT: A 795 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8684 (mt-10) outliers start: 5 outliers final: 1 residues processed: 304 average time/residue: 0.3348 time to fit residues: 148.5898 Evaluate side-chains 182 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 242 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 9.9990 chunk 155 optimal weight: 30.0000 chunk 86 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 160 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 348 ASN B 363 GLN ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 204 GLN C 221 GLN C 250 HIS C 302 HIS C 591 HIS C 690 GLN C 715 HIS D 35 ASN D 157 ASN D 169 GLN D 240 ASN D 242 GLN D 274 GLN D 399 HIS ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 150 ASN E 202 GLN ** E 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 423 GLN E 433 GLN A 662 HIS A 809 HIS A 838 GLN A 902 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17856 Z= 0.198 Angle : 0.670 10.223 24425 Z= 0.354 Chirality : 0.041 0.230 2811 Planarity : 0.004 0.050 2871 Dihedral : 20.009 81.048 3005 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.66 % Allowed : 13.76 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -1.09 (0.18), residues: 1961 helix: -0.63 (0.13), residues: 1182 sheet: -2.74 (0.34), residues: 164 loop : 0.16 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 191 HIS 0.008 0.001 HIS A 560 PHE 0.017 0.001 PHE C 49 TYR 0.021 0.001 TYR C 255 ARG 0.006 0.000 ARG E 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 2.026 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: B 334 GLU cc_start: 0.9543 (tm-30) cc_final: 0.9321 (pt0) REVERT: B 335 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8919 (mp0) REVERT: B 342 LYS cc_start: 0.9496 (tttm) cc_final: 0.9066 (ptpp) REVERT: B 343 TRP cc_start: 0.9235 (m-10) cc_final: 0.8740 (m100) REVERT: B 417 MET cc_start: 0.8933 (mmt) cc_final: 0.8693 (ptm) REVERT: B 421 GLU cc_start: 0.8543 (mt-10) cc_final: 0.8161 (mt-10) REVERT: B 443 ARG cc_start: 0.9228 (mtt180) cc_final: 0.8993 (mtt90) REVERT: B 483 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8418 (m-10) REVERT: B 493 MET cc_start: 0.7997 (mmt) cc_final: 0.7097 (tmm) REVERT: C 132 LEU cc_start: 0.9280 (tp) cc_final: 0.9043 (tp) REVERT: C 208 ILE cc_start: 0.9612 (mt) cc_final: 0.9375 (tp) REVERT: C 323 MET cc_start: 0.9283 (tmm) cc_final: 0.9022 (tmm) REVERT: C 340 LYS cc_start: 0.9734 (tptp) cc_final: 0.9397 (tptp) REVERT: C 381 ASP cc_start: 0.9140 (t0) cc_final: 0.8890 (t0) REVERT: C 395 ASP cc_start: 0.9178 (t70) cc_final: 0.8808 (p0) REVERT: C 443 GLU cc_start: 0.9681 (mt-10) cc_final: 0.9283 (tt0) REVERT: C 658 MET cc_start: 0.8959 (tpt) cc_final: 0.8596 (tpt) REVERT: D 46 MET cc_start: 0.9238 (mpp) cc_final: 0.8812 (mpp) REVERT: D 335 ASP cc_start: 0.9049 (m-30) cc_final: 0.8676 (p0) REVERT: D 346 LEU cc_start: 0.9425 (tp) cc_final: 0.9223 (tt) REVERT: D 426 MET cc_start: 0.9347 (mmm) cc_final: 0.8995 (mmm) REVERT: E 237 PHE cc_start: 0.8635 (m-10) cc_final: 0.8116 (m-10) REVERT: A 588 ASP cc_start: 0.8634 (m-30) cc_final: 0.8129 (p0) REVERT: A 790 CYS cc_start: 0.9640 (m) cc_final: 0.9420 (m) REVERT: A 795 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8675 (mt-10) REVERT: A 828 ASN cc_start: 0.9275 (t0) cc_final: 0.8909 (t0) outliers start: 29 outliers final: 15 residues processed: 218 average time/residue: 0.3022 time to fit residues: 100.7651 Evaluate side-chains 183 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 167 time to evaluate : 2.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 625 MET Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 103 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 154 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 166 optimal weight: 0.9990 chunk 184 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 200 HIS ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17856 Z= 0.249 Angle : 0.647 9.375 24425 Z= 0.342 Chirality : 0.041 0.252 2811 Planarity : 0.004 0.049 2871 Dihedral : 19.900 84.584 3003 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.74 % Allowed : 15.13 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: -0.22 (0.19), residues: 1961 helix: 0.30 (0.15), residues: 1180 sheet: -2.69 (0.34), residues: 177 loop : 0.14 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 191 HIS 0.006 0.001 HIS A 560 PHE 0.018 0.001 PHE C 49 TYR 0.017 0.001 TYR A 579 ARG 0.018 0.000 ARG C 603 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 169 time to evaluate : 2.071 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: B 335 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8930 (mp0) REVERT: B 342 LYS cc_start: 0.9477 (tttm) cc_final: 0.9081 (ptpp) REVERT: B 343 TRP cc_start: 0.9270 (m-10) cc_final: 0.8738 (m100) REVERT: B 421 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8226 (mt-10) REVERT: B 443 ARG cc_start: 0.9314 (mtt180) cc_final: 0.9022 (mtt90) REVERT: B 456 ARG cc_start: 0.9006 (tpt-90) cc_final: 0.8748 (tpp80) REVERT: B 483 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.8467 (m-10) REVERT: B 493 MET cc_start: 0.8073 (mmt) cc_final: 0.7261 (tmm) REVERT: C 132 LEU cc_start: 0.9241 (tp) cc_final: 0.8915 (tp) REVERT: C 208 ILE cc_start: 0.9588 (mt) cc_final: 0.9325 (tp) REVERT: C 222 ASP cc_start: 0.9210 (m-30) cc_final: 0.8941 (p0) REVERT: C 323 MET cc_start: 0.9256 (tmm) cc_final: 0.8978 (tmm) REVERT: C 443 GLU cc_start: 0.9696 (mt-10) cc_final: 0.9283 (tt0) REVERT: C 658 MET cc_start: 0.8885 (tpt) cc_final: 0.8546 (tpt) REVERT: D 46 MET cc_start: 0.9292 (mpp) cc_final: 0.8753 (mpp) REVERT: D 335 ASP cc_start: 0.9138 (m-30) cc_final: 0.8780 (p0) REVERT: D 346 LEU cc_start: 0.9442 (tp) cc_final: 0.9237 (tt) REVERT: D 426 MET cc_start: 0.9429 (mmm) cc_final: 0.8929 (mmm) REVERT: E 237 PHE cc_start: 0.8719 (m-10) cc_final: 0.8208 (m-10) REVERT: A 524 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8093 (ptm) REVERT: A 588 ASP cc_start: 0.8659 (m-30) cc_final: 0.8213 (p0) REVERT: A 630 LEU cc_start: 0.9166 (tp) cc_final: 0.8878 (tp) REVERT: A 750 LEU cc_start: 0.9527 (mt) cc_final: 0.8665 (tp) REVERT: A 790 CYS cc_start: 0.9662 (m) cc_final: 0.9440 (m) REVERT: A 795 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8564 (mp0) REVERT: A 828 ASN cc_start: 0.9277 (t0) cc_final: 0.8987 (t0) outliers start: 48 outliers final: 25 residues processed: 204 average time/residue: 0.2983 time to fit residues: 93.9035 Evaluate side-chains 185 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 158 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 334 LEU Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 0.6980 chunk 140 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 187 optimal weight: 0.6980 chunk 198 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 177 optimal weight: 8.9990 chunk 53 optimal weight: 0.0270 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 GLN ** C 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17856 Z= 0.152 Angle : 0.607 11.226 24425 Z= 0.315 Chirality : 0.040 0.294 2811 Planarity : 0.004 0.055 2871 Dihedral : 19.716 87.047 3003 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.94 % Allowed : 15.65 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.09 (0.19), residues: 1961 helix: 0.55 (0.15), residues: 1189 sheet: -2.47 (0.36), residues: 171 loop : 0.20 (0.27), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 57 HIS 0.006 0.001 HIS B 461 PHE 0.020 0.001 PHE C 668 TYR 0.021 0.001 TYR A 698 ARG 0.009 0.000 ARG C 669 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 181 time to evaluate : 1.904 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: B 334 GLU cc_start: 0.9522 (tm-30) cc_final: 0.9310 (pt0) REVERT: B 335 GLU cc_start: 0.9232 (mm-30) cc_final: 0.8844 (mp0) REVERT: B 342 LYS cc_start: 0.9418 (tttm) cc_final: 0.9034 (mtmm) REVERT: B 443 ARG cc_start: 0.9323 (mtt180) cc_final: 0.8984 (mtt90) REVERT: B 483 PHE cc_start: 0.8571 (OUTLIER) cc_final: 0.8206 (m-10) REVERT: B 493 MET cc_start: 0.8092 (mmt) cc_final: 0.7270 (tmm) REVERT: C 47 GLN cc_start: 0.8935 (mm-40) cc_final: 0.8399 (mt0) REVERT: C 132 LEU cc_start: 0.9179 (tp) cc_final: 0.8839 (tp) REVERT: C 208 ILE cc_start: 0.9569 (mt) cc_final: 0.9315 (tp) REVERT: C 323 MET cc_start: 0.9255 (tmm) cc_final: 0.9006 (tmm) REVERT: C 381 ASP cc_start: 0.9072 (t0) cc_final: 0.8802 (t0) REVERT: C 443 GLU cc_start: 0.9692 (mt-10) cc_final: 0.9471 (mt-10) REVERT: C 658 MET cc_start: 0.8792 (tpt) cc_final: 0.8486 (tpt) REVERT: D 46 MET cc_start: 0.9297 (mpp) cc_final: 0.8729 (mpp) REVERT: D 214 ASP cc_start: 0.9307 (OUTLIER) cc_final: 0.9016 (p0) REVERT: D 335 ASP cc_start: 0.9013 (m-30) cc_final: 0.8645 (p0) REVERT: D 346 LEU cc_start: 0.9467 (tp) cc_final: 0.9262 (tt) REVERT: D 426 MET cc_start: 0.9389 (mmm) cc_final: 0.8913 (mmm) REVERT: E 143 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9377 (mm) REVERT: E 237 PHE cc_start: 0.8642 (m-10) cc_final: 0.8156 (m-10) REVERT: A 524 MET cc_start: 0.8746 (tpt) cc_final: 0.7992 (ptp) REVERT: A 588 ASP cc_start: 0.8563 (m-30) cc_final: 0.8145 (p0) REVERT: A 630 LEU cc_start: 0.9111 (tp) cc_final: 0.8774 (tp) REVERT: A 750 LEU cc_start: 0.9483 (mt) cc_final: 0.8631 (tp) REVERT: A 790 CYS cc_start: 0.9645 (m) cc_final: 0.9432 (m) REVERT: A 795 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8572 (mp0) REVERT: A 828 ASN cc_start: 0.9227 (t0) cc_final: 0.8770 (t0) outliers start: 34 outliers final: 21 residues processed: 204 average time/residue: 0.2940 time to fit residues: 92.1336 Evaluate side-chains 185 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 407 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 840 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 165 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 147 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 136 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 50 optimal weight: 0.3980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 HIS ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17856 Z= 0.189 Angle : 0.592 8.430 24425 Z= 0.310 Chirality : 0.038 0.168 2811 Planarity : 0.004 0.042 2871 Dihedral : 19.596 88.248 3003 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.17 % Allowed : 17.36 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.45 (0.20), residues: 1961 helix: 0.89 (0.15), residues: 1183 sheet: -2.38 (0.37), residues: 171 loop : 0.22 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 57 HIS 0.004 0.001 HIS B 461 PHE 0.012 0.001 PHE C 49 TYR 0.020 0.001 TYR A 579 ARG 0.004 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 165 time to evaluate : 2.177 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: B 342 LYS cc_start: 0.9440 (tttm) cc_final: 0.9022 (mtmm) REVERT: B 483 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8377 (m-10) REVERT: B 493 MET cc_start: 0.8334 (mmt) cc_final: 0.7224 (tmm) REVERT: C 47 GLN cc_start: 0.8698 (mm-40) cc_final: 0.8347 (mt0) REVERT: C 132 LEU cc_start: 0.9213 (tp) cc_final: 0.8829 (tp) REVERT: C 208 ILE cc_start: 0.9576 (mt) cc_final: 0.9345 (tp) REVERT: C 222 ASP cc_start: 0.9178 (m-30) cc_final: 0.8830 (p0) REVERT: C 323 MET cc_start: 0.9244 (tmm) cc_final: 0.8977 (tmm) REVERT: C 381 ASP cc_start: 0.9062 (t0) cc_final: 0.8787 (t70) REVERT: C 443 GLU cc_start: 0.9694 (mt-10) cc_final: 0.9469 (mt-10) REVERT: C 658 MET cc_start: 0.8781 (tpt) cc_final: 0.8469 (tpt) REVERT: D 46 MET cc_start: 0.9303 (mpp) cc_final: 0.8768 (mpp) REVERT: D 214 ASP cc_start: 0.9339 (OUTLIER) cc_final: 0.8996 (p0) REVERT: D 335 ASP cc_start: 0.9087 (m-30) cc_final: 0.8728 (p0) REVERT: D 346 LEU cc_start: 0.9474 (tp) cc_final: 0.9261 (tt) REVERT: D 426 MET cc_start: 0.9406 (mmm) cc_final: 0.8878 (mmm) REVERT: E 237 PHE cc_start: 0.8676 (m-10) cc_final: 0.8221 (m-10) REVERT: A 524 MET cc_start: 0.8765 (tpt) cc_final: 0.8291 (ptp) REVERT: A 588 ASP cc_start: 0.8604 (m-30) cc_final: 0.8175 (p0) REVERT: A 630 LEU cc_start: 0.9175 (tp) cc_final: 0.8921 (tp) REVERT: A 750 LEU cc_start: 0.9480 (mt) cc_final: 0.8587 (tt) REVERT: A 790 CYS cc_start: 0.9666 (m) cc_final: 0.9455 (m) REVERT: A 795 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8573 (mp0) REVERT: A 828 ASN cc_start: 0.9247 (t0) cc_final: 0.8966 (t0) outliers start: 38 outliers final: 28 residues processed: 191 average time/residue: 0.2965 time to fit residues: 89.1963 Evaluate side-chains 186 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 2.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 66 optimal weight: 1.9990 chunk 178 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 164 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 104 optimal weight: 8.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17856 Z= 0.242 Angle : 0.614 11.228 24425 Z= 0.322 Chirality : 0.039 0.334 2811 Planarity : 0.004 0.047 2871 Dihedral : 19.598 89.782 3003 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.80 % Allowed : 17.48 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.54 (0.19), residues: 1961 helix: 0.99 (0.15), residues: 1179 sheet: -2.13 (0.38), residues: 164 loop : 0.08 (0.27), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 57 HIS 0.006 0.001 HIS B 461 PHE 0.012 0.001 PHE C 49 TYR 0.022 0.001 TYR A 579 ARG 0.004 0.000 ARG E 284 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 161 time to evaluate : 1.923 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: B 342 LYS cc_start: 0.9452 (tttm) cc_final: 0.9041 (mtmm) REVERT: B 441 MET cc_start: 0.8807 (mtp) cc_final: 0.8238 (pmm) REVERT: B 483 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.8499 (m-10) REVERT: B 493 MET cc_start: 0.8402 (mmt) cc_final: 0.7213 (tmm) REVERT: C 47 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8390 (mt0) REVERT: C 222 ASP cc_start: 0.9179 (m-30) cc_final: 0.8742 (p0) REVERT: C 323 MET cc_start: 0.9234 (tmm) cc_final: 0.8959 (tmm) REVERT: C 381 ASP cc_start: 0.9075 (t0) cc_final: 0.8804 (t70) REVERT: C 658 MET cc_start: 0.8832 (tpt) cc_final: 0.8540 (tpt) REVERT: D 46 MET cc_start: 0.9301 (mpp) cc_final: 0.8722 (mpp) REVERT: D 214 ASP cc_start: 0.9363 (OUTLIER) cc_final: 0.9035 (p0) REVERT: D 335 ASP cc_start: 0.9124 (m-30) cc_final: 0.8795 (p0) REVERT: D 346 LEU cc_start: 0.9481 (tp) cc_final: 0.9260 (tt) REVERT: D 426 MET cc_start: 0.9423 (mmm) cc_final: 0.8850 (mmm) REVERT: E 237 PHE cc_start: 0.8711 (m-10) cc_final: 0.8229 (m-10) REVERT: A 588 ASP cc_start: 0.8638 (m-30) cc_final: 0.8168 (p0) REVERT: A 630 LEU cc_start: 0.9210 (tp) cc_final: 0.8998 (tp) REVERT: A 750 LEU cc_start: 0.9493 (mt) cc_final: 0.8642 (tt) REVERT: A 795 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8699 (mt-10) REVERT: A 828 ASN cc_start: 0.9234 (t0) cc_final: 0.8911 (t0) outliers start: 49 outliers final: 34 residues processed: 195 average time/residue: 0.2817 time to fit residues: 86.6419 Evaluate side-chains 187 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 151 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 622 ASN Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 191 optimal weight: 3.9990 chunk 22 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 120 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17856 Z= 0.183 Angle : 0.594 9.186 24425 Z= 0.309 Chirality : 0.039 0.305 2811 Planarity : 0.003 0.047 2871 Dihedral : 19.528 90.162 3003 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.68 % Allowed : 18.39 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.64 (0.20), residues: 1961 helix: 1.09 (0.15), residues: 1183 sheet: -2.13 (0.37), residues: 176 loop : 0.14 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 57 HIS 0.006 0.001 HIS B 461 PHE 0.011 0.001 PHE E 163 TYR 0.022 0.001 TYR A 579 ARG 0.003 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 159 time to evaluate : 2.092 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: B 342 LYS cc_start: 0.9467 (tttm) cc_final: 0.9076 (mtmm) REVERT: B 441 MET cc_start: 0.8791 (mtp) cc_final: 0.8207 (pmm) REVERT: B 483 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8450 (m-10) REVERT: B 493 MET cc_start: 0.8432 (mmt) cc_final: 0.7172 (tmm) REVERT: C 47 GLN cc_start: 0.8626 (mm-40) cc_final: 0.8268 (mt0) REVERT: C 132 LEU cc_start: 0.9153 (tp) cc_final: 0.8744 (tp) REVERT: C 222 ASP cc_start: 0.9090 (m-30) cc_final: 0.8739 (p0) REVERT: C 323 MET cc_start: 0.9222 (tmm) cc_final: 0.8963 (tmm) REVERT: C 381 ASP cc_start: 0.9066 (t0) cc_final: 0.8795 (t70) REVERT: C 443 GLU cc_start: 0.9694 (mt-10) cc_final: 0.9458 (mt-10) REVERT: C 652 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6452 (p-80) REVERT: C 658 MET cc_start: 0.8794 (tpt) cc_final: 0.8496 (tpt) REVERT: D 46 MET cc_start: 0.9306 (mpp) cc_final: 0.8710 (mpp) REVERT: D 214 ASP cc_start: 0.9357 (OUTLIER) cc_final: 0.9031 (p0) REVERT: D 335 ASP cc_start: 0.9085 (m-30) cc_final: 0.8731 (p0) REVERT: D 346 LEU cc_start: 0.9477 (tp) cc_final: 0.9266 (tt) REVERT: D 426 MET cc_start: 0.9399 (mmm) cc_final: 0.8842 (mmm) REVERT: E 143 LEU cc_start: 0.9666 (OUTLIER) cc_final: 0.9379 (mm) REVERT: E 237 PHE cc_start: 0.8659 (m-10) cc_final: 0.8202 (m-10) REVERT: E 293 ARG cc_start: 0.6323 (OUTLIER) cc_final: 0.6009 (tpp-160) REVERT: A 588 ASP cc_start: 0.8639 (m-30) cc_final: 0.8227 (p0) REVERT: A 750 LEU cc_start: 0.9483 (mt) cc_final: 0.8628 (tt) REVERT: A 828 ASN cc_start: 0.9211 (t0) cc_final: 0.8851 (t0) outliers start: 47 outliers final: 35 residues processed: 191 average time/residue: 0.2751 time to fit residues: 83.6089 Evaluate side-chains 193 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 153 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 487 CYS Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain E residue 401 CYS Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 122 optimal weight: 5.9990 chunk 78 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 59 optimal weight: 0.0770 chunk 38 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 179 optimal weight: 5.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17856 Z= 0.186 Angle : 0.604 14.180 24425 Z= 0.310 Chirality : 0.040 0.348 2811 Planarity : 0.003 0.048 2871 Dihedral : 19.479 90.394 3003 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.68 % Allowed : 18.90 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.75 (0.20), residues: 1961 helix: 1.14 (0.15), residues: 1191 sheet: -1.70 (0.40), residues: 160 loop : 0.06 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 57 HIS 0.006 0.001 HIS B 461 PHE 0.015 0.001 PHE B 385 TYR 0.020 0.001 TYR A 698 ARG 0.005 0.000 ARG C 711 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 153 time to evaluate : 1.919 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: B 342 LYS cc_start: 0.9474 (tttm) cc_final: 0.9036 (mtmm) REVERT: B 441 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8264 (pmm) REVERT: B 483 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8472 (m-10) REVERT: B 493 MET cc_start: 0.8411 (mmt) cc_final: 0.7874 (tmm) REVERT: C 47 GLN cc_start: 0.8629 (mm-40) cc_final: 0.8275 (mt0) REVERT: C 132 LEU cc_start: 0.9157 (tp) cc_final: 0.8741 (tp) REVERT: C 222 ASP cc_start: 0.9095 (m-30) cc_final: 0.8746 (p0) REVERT: C 323 MET cc_start: 0.9222 (tmm) cc_final: 0.8931 (tmm) REVERT: C 381 ASP cc_start: 0.9059 (t0) cc_final: 0.8788 (t70) REVERT: C 443 GLU cc_start: 0.9695 (mt-10) cc_final: 0.9462 (mt-10) REVERT: C 652 HIS cc_start: 0.7076 (OUTLIER) cc_final: 0.6477 (p-80) REVERT: C 658 MET cc_start: 0.8780 (tpt) cc_final: 0.8482 (tpt) REVERT: D 46 MET cc_start: 0.9302 (mpp) cc_final: 0.8698 (mpp) REVERT: D 214 ASP cc_start: 0.9368 (OUTLIER) cc_final: 0.9048 (p0) REVERT: D 335 ASP cc_start: 0.9078 (m-30) cc_final: 0.8745 (p0) REVERT: D 346 LEU cc_start: 0.9492 (tp) cc_final: 0.9263 (tt) REVERT: D 385 MET cc_start: 0.9324 (mmm) cc_final: 0.9043 (mpp) REVERT: D 426 MET cc_start: 0.9409 (mmm) cc_final: 0.8826 (mmm) REVERT: E 143 LEU cc_start: 0.9672 (OUTLIER) cc_final: 0.9382 (mm) REVERT: E 151 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8638 (mt) REVERT: E 237 PHE cc_start: 0.8674 (m-80) cc_final: 0.8284 (m-10) REVERT: E 293 ARG cc_start: 0.6307 (OUTLIER) cc_final: 0.5985 (tpp-160) REVERT: A 588 ASP cc_start: 0.8646 (m-30) cc_final: 0.8237 (p0) REVERT: A 750 LEU cc_start: 0.9472 (mt) cc_final: 0.8641 (tt) REVERT: A 828 ASN cc_start: 0.9208 (t0) cc_final: 0.8842 (t0) outliers start: 47 outliers final: 33 residues processed: 185 average time/residue: 0.2774 time to fit residues: 81.4694 Evaluate side-chains 192 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 152 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain C residue 662 PHE Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 400 THR Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 840 ILE Chi-restraints excluded: chain A residue 882 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 189 optimal weight: 2.9990 chunk 172 optimal weight: 0.8980 chunk 184 optimal weight: 0.3980 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 166 optimal weight: 0.0770 chunk 174 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 overall best weight: 0.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 362 HIS ** B 461 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17856 Z= 0.151 Angle : 0.609 13.145 24425 Z= 0.308 Chirality : 0.040 0.383 2811 Planarity : 0.003 0.048 2871 Dihedral : 19.335 89.390 3003 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.23 % Allowed : 19.53 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.20), residues: 1961 helix: 1.22 (0.16), residues: 1189 sheet: -1.49 (0.41), residues: 160 loop : 0.08 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 57 HIS 0.006 0.001 HIS B 461 PHE 0.011 0.001 PHE E 163 TYR 0.026 0.001 TYR A 579 ARG 0.005 0.000 ARG A 528 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 1.994 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: B 342 LYS cc_start: 0.9464 (tttm) cc_final: 0.9037 (mtmm) REVERT: B 441 MET cc_start: 0.8823 (mtp) cc_final: 0.8463 (pmm) REVERT: B 483 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8436 (m-10) REVERT: C 47 GLN cc_start: 0.8599 (mm-40) cc_final: 0.8277 (mt0) REVERT: C 132 LEU cc_start: 0.9114 (tp) cc_final: 0.8718 (tp) REVERT: C 222 ASP cc_start: 0.9080 (m-30) cc_final: 0.8721 (p0) REVERT: C 323 MET cc_start: 0.9237 (tmm) cc_final: 0.8950 (tmm) REVERT: C 381 ASP cc_start: 0.9050 (t0) cc_final: 0.8766 (t70) REVERT: C 428 GLU cc_start: 0.9458 (mt-10) cc_final: 0.9128 (mp0) REVERT: C 443 GLU cc_start: 0.9695 (mt-10) cc_final: 0.9480 (mt-10) REVERT: C 652 HIS cc_start: 0.7094 (OUTLIER) cc_final: 0.6452 (p-80) REVERT: C 658 MET cc_start: 0.8710 (tpt) cc_final: 0.8422 (tpt) REVERT: D 46 MET cc_start: 0.9291 (mpp) cc_final: 0.8655 (mpp) REVERT: D 214 ASP cc_start: 0.9349 (OUTLIER) cc_final: 0.9020 (p0) REVERT: D 239 TYR cc_start: 0.9056 (m-10) cc_final: 0.8794 (m-10) REVERT: D 335 ASP cc_start: 0.8987 (m-30) cc_final: 0.8654 (p0) REVERT: D 426 MET cc_start: 0.9396 (mmm) cc_final: 0.8856 (mmm) REVERT: D 440 MET cc_start: 0.9023 (mmm) cc_final: 0.8759 (mmm) REVERT: E 143 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9337 (mm) REVERT: E 151 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8640 (mt) REVERT: E 237 PHE cc_start: 0.8609 (m-80) cc_final: 0.8300 (m-10) REVERT: E 293 ARG cc_start: 0.6370 (OUTLIER) cc_final: 0.5994 (tpp-160) REVERT: A 588 ASP cc_start: 0.8607 (m-30) cc_final: 0.8198 (p0) REVERT: A 750 LEU cc_start: 0.9448 (mt) cc_final: 0.8602 (tt) REVERT: A 828 ASN cc_start: 0.9211 (t0) cc_final: 0.8856 (t0) outliers start: 39 outliers final: 27 residues processed: 195 average time/residue: 0.2909 time to fit residues: 89.3114 Evaluate side-chains 188 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 155 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 LEU Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 280 ASP Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 349 CYS Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain E residue 329 LEU Chi-restraints excluded: chain E residue 419 VAL Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 719 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 194 optimal weight: 0.2980 chunk 118 optimal weight: 4.9990 chunk 92 optimal weight: 0.8980 chunk 135 optimal weight: 8.9990 chunk 204 optimal weight: 10.0000 chunk 187 optimal weight: 0.0070 chunk 162 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 461 HIS ** C 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 838 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 17856 Z= 0.152 Angle : 0.623 13.894 24425 Z= 0.313 Chirality : 0.040 0.414 2811 Planarity : 0.003 0.049 2871 Dihedral : 19.247 88.968 3003 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.83 % Allowed : 20.33 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % 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: 0.86 (0.20), residues: 1961 helix: 1.20 (0.15), residues: 1193 sheet: -1.44 (0.42), residues: 155 loop : 0.09 (0.27), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 57 HIS 0.009 0.001 HIS C 615 PHE 0.010 0.001 PHE E 163 TYR 0.025 0.001 TYR A 579 ARG 0.004 0.000 ARG A 528 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3922 Ramachandran restraints generated. 1961 Oldfield, 0 Emsley, 1961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 2.090 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: B 334 GLU cc_start: 0.9463 (tm-30) cc_final: 0.9239 (tm-30) REVERT: B 342 LYS cc_start: 0.9442 (tttm) cc_final: 0.9037 (mtmm) REVERT: B 441 MET cc_start: 0.8826 (mtp) cc_final: 0.8471 (pmm) REVERT: B 483 PHE cc_start: 0.8695 (OUTLIER) cc_final: 0.8429 (m-10) REVERT: C 47 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8303 (mt0) REVERT: C 323 MET cc_start: 0.9216 (tmm) cc_final: 0.8950 (tmm) REVERT: C 381 ASP cc_start: 0.9017 (t0) cc_final: 0.8730 (t70) REVERT: C 428 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9128 (mp0) REVERT: C 443 GLU cc_start: 0.9695 (mt-10) cc_final: 0.9489 (mt-10) REVERT: C 625 MET cc_start: 0.8070 (ptt) cc_final: 0.7567 (pmm) REVERT: C 652 HIS cc_start: 0.7095 (OUTLIER) cc_final: 0.6471 (p-80) REVERT: C 658 MET cc_start: 0.8688 (tpt) cc_final: 0.8416 (tpt) REVERT: D 46 MET cc_start: 0.9278 (mpp) cc_final: 0.8635 (mpp) REVERT: D 53 LEU cc_start: 0.9563 (tp) cc_final: 0.9120 (mt) REVERT: D 214 ASP cc_start: 0.9359 (OUTLIER) cc_final: 0.9043 (p0) REVERT: D 239 TYR cc_start: 0.9024 (m-10) cc_final: 0.8761 (m-10) REVERT: D 335 ASP cc_start: 0.9004 (m-30) cc_final: 0.8647 (p0) REVERT: D 385 MET cc_start: 0.9341 (mmm) cc_final: 0.8963 (mpp) REVERT: D 426 MET cc_start: 0.9395 (mmm) cc_final: 0.8849 (mmm) REVERT: E 143 LEU cc_start: 0.9632 (OUTLIER) cc_final: 0.9328 (mm) REVERT: E 151 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8637 (mt) REVERT: E 237 PHE cc_start: 0.8607 (m-80) cc_final: 0.8336 (m-10) REVERT: E 413 LEU cc_start: 0.9627 (mp) cc_final: 0.9315 (mt) REVERT: A 536 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7234 (mtm) REVERT: A 588 ASP cc_start: 0.8616 (m-30) cc_final: 0.8221 (p0) REVERT: A 750 LEU cc_start: 0.9439 (mt) cc_final: 0.8604 (tt) REVERT: A 828 ASN cc_start: 0.9226 (t0) cc_final: 0.8878 (t0) outliers start: 32 outliers final: 23 residues processed: 177 average time/residue: 0.2885 time to fit residues: 82.8330 Evaluate side-chains 181 residues out of total 1751 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 403 ASP Chi-restraints excluded: chain B residue 450 ILE Chi-restraints excluded: chain B residue 454 LEU Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 LEU Chi-restraints excluded: chain B residue 483 PHE Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 114 PHE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 647 VAL Chi-restraints excluded: chain C residue 652 HIS Chi-restraints excluded: chain D residue 74 LEU Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 214 ASP Chi-restraints excluded: chain D residue 388 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 259 LEU Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 681 LEU Chi-restraints excluded: chain A residue 719 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 8.9990 chunk 49 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 162 optimal weight: 0.0010 chunk 68 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 421 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.062142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.044912 restraints weight = 87732.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.046289 restraints weight = 50024.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.047236 restraints weight = 34001.324| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17856 Z= 0.156 Angle : 0.631 13.233 24425 Z= 0.315 Chirality : 0.040 0.380 2811 Planarity : 0.003 0.048 2871 Dihedral : 19.169 88.251 3003 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.83 % Allowed : 20.45 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.20), residues: 1961 helix: 1.21 (0.15), residues: 1192 sheet: -1.40 (0.42), residues: 155 loop : 0.11 (0.27), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 57 HIS 0.003 0.001 HIS C 580 PHE 0.010 0.001 PHE E 163 TYR 0.026 0.001 TYR A 579 ARG 0.005 0.000 ARG A 528 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3360.93 seconds wall clock time: 62 minutes 34.76 seconds (3754.76 seconds total)