Starting phenix.real_space_refine on Sat Mar 16 21:14:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/03_2024/8h77_34519_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/03_2024/8h77_34519.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/03_2024/8h77_34519.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/03_2024/8h77_34519.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/03_2024/8h77_34519_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h77_34519/03_2024/8h77_34519_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 7 Type Number sf(0) Gaussians P 4 5.49 5 S 76 5.16 5 Be 2 3.05 5 C 9939 2.51 5 N 2698 2.21 5 O 3001 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 13": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 195": "OE1" <-> "OE2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 303": "OE1" <-> "OE2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A GLU 554": "OE1" <-> "OE2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 153": "OE1" <-> "OE2" Residue "B GLU 299": "OE1" <-> "OE2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B GLU 384": "OE1" <-> "OE2" Residue "B GLU 418": "OE1" <-> "OE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B GLU 478": "OE1" <-> "OE2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B GLU 569": "OE1" <-> "OE2" Residue "C GLU 32": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E GLU 384": "OE1" <-> "OE2" Residue "E GLU 387": "OE1" <-> "OE2" Residue "E GLU 404": "OE1" <-> "OE2" Residue "F PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F GLU 185": "OE1" <-> "OE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 310": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15726 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 5158 Classifications: {'peptide': 636} Link IDs: {'PTRANS': 17, 'TRANS': 618} Chain breaks: 1 Chain: "B" Number of atoms: 5012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 5012 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 17, 'TRANS': 602} Chain breaks: 1 Chain: "C" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 942 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "D" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 928 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "E" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1134 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 5, 'TRANS': 134} Chain: "F" Number of atoms: 2490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2490 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 295} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.32, per 1000 atoms: 0.53 Number of scatterers: 15726 At special positions: 0 Unit cell: (113.42, 142.31, 138.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 76 16.00 P 4 15.00 F 6 9.00 O 3001 8.00 N 2698 7.00 C 9939 6.00 Be 2 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.67 Conformation dependent library (CDL) restraints added in 2.7 seconds 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3676 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 15 sheets defined 34.9% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.17 Creating SS restraints... Processing helix chain 'A' and resid 21 through 30 Processing helix chain 'A' and resid 38 through 60 removed outlier: 4.171A pdb=" N THR A 60 " --> pdb=" O TYR A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 133 through 138 removed outlier: 3.511A pdb=" N TYR A 137 " --> pdb=" O TYR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 300 through 309 Processing helix chain 'A' and resid 398 through 421 Processing helix chain 'A' and resid 423 through 443 removed outlier: 4.218A pdb=" N LYS A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYS A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 432 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 470 through 474 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 498 through 505 removed outlier: 3.746A pdb=" N GLU A 501 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ARG A 502 " --> pdb=" O PHE A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 Processing helix chain 'A' and resid 549 through 570 removed outlier: 4.932A pdb=" N ASN A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LEU A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 570 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 606 removed outlier: 3.616A pdb=" N ARG A 604 " --> pdb=" O ALA A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 618 removed outlier: 4.285A pdb=" N GLY A 618 " --> pdb=" O SER A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 615 through 618' Processing helix chain 'A' and resid 633 through 644 removed outlier: 3.753A pdb=" N ALA A 644 " --> pdb=" O GLN A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 665 removed outlier: 4.086A pdb=" N LEU A 664 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N SER A 665 " --> pdb=" O THR A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 38 through 59 Processing helix chain 'B' and resid 62 through 66 removed outlier: 3.716A pdb=" N LEU B 65 " --> pdb=" O PRO B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 101 Processing helix chain 'B' and resid 109 through 116 removed outlier: 3.607A pdb=" N ALA B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 399 through 421 removed outlier: 3.610A pdb=" N SER B 417 " --> pdb=" O LEU B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 443 removed outlier: 4.331A pdb=" N ALA B 432 " --> pdb=" O LYS B 428 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 451 No H-bonds generated for 'chain 'B' and resid 448 through 451' Processing helix chain 'B' and resid 470 through 475 Processing helix chain 'B' and resid 491 through 494 No H-bonds generated for 'chain 'B' and resid 491 through 494' Processing helix chain 'B' and resid 501 through 505 Processing helix chain 'B' and resid 516 through 525 removed outlier: 4.165A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 558 removed outlier: 3.693A pdb=" N LYS B 552 " --> pdb=" O GLU B 548 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU B 554 " --> pdb=" O LYS B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 571 Processing helix chain 'B' and resid 600 through 608 removed outlier: 4.270A pdb=" N ALA B 608 " --> pdb=" O ARG B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 620 removed outlier: 3.552A pdb=" N MET B 617 " --> pdb=" O ASN B 614 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLY B 618 " --> pdb=" O SER B 615 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR B 619 " --> pdb=" O THR B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 644 removed outlier: 3.791A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 665 Processing helix chain 'B' and resid 673 through 688 Processing helix chain 'E' and resid 296 through 301 removed outlier: 3.690A pdb=" N LEU E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 321 through 324 No H-bonds generated for 'chain 'E' and resid 321 through 324' Processing helix chain 'E' and resid 328 through 336 removed outlier: 4.119A pdb=" N ARG E 333 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 382 through 390 Processing helix chain 'E' and resid 392 through 394 No H-bonds generated for 'chain 'E' and resid 392 through 394' Processing helix chain 'F' and resid 3 through 9 Processing helix chain 'F' and resid 71 through 79 removed outlier: 3.554A pdb=" N CYS F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 108 removed outlier: 3.571A pdb=" N SER F 104 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 143 Processing helix chain 'F' and resid 173 through 192 Proline residue: F 180 - end of helix Processing helix chain 'F' and resid 196 through 215 removed outlier: 4.075A pdb=" N LYS F 215 " --> pdb=" O ASN F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 244 Proline residue: F 232 - end of helix removed outlier: 3.685A pdb=" N CYS F 240 " --> pdb=" O ASN F 236 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS F 241 " --> pdb=" O TYR F 237 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU F 242 " --> pdb=" O CYS F 238 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N VAL F 243 " --> pdb=" O GLN F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 259 removed outlier: 3.876A pdb=" N ASN F 259 " --> pdb=" O SER F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 278 removed outlier: 4.593A pdb=" N ARG F 271 " --> pdb=" O ALA F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 294 removed outlier: 3.516A pdb=" N LYS F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 319 Processing helix chain 'F' and resid 321 through 328 removed outlier: 3.772A pdb=" N PHE F 324 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG F 325 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY F 326 " --> pdb=" O ARG F 323 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE F 328 " --> pdb=" O ARG F 325 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 278 through 281 removed outlier: 3.777A pdb=" N LEU A 217 " --> pdb=" O ASP A 278 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE A 73 " --> pdb=" O THR A 214 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N TYR A 216 " --> pdb=" O ILE A 73 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N ILE A 75 " --> pdb=" O TYR A 216 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 83 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 220 through 223 removed outlier: 3.757A pdb=" N ARG A 221 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU A 274 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LYS A 223 " --> pdb=" O ILE A 272 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ILE A 272 " --> pdb=" O LYS A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 360 through 363 removed outlier: 7.105A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LYS A 354 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N GLY A 379 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N TYR A 356 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL A 381 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 532 through 535 Processing sheet with id= E, first strand: chain 'B' and resid 73 through 76 removed outlier: 3.527A pdb=" N THR B 179 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 360 through 363 removed outlier: 7.130A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N LYS B 354 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLY B 379 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N TYR B 356 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL B 381 " --> pdb=" O TYR B 356 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE B 335 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 533 through 535 removed outlier: 5.893A pdb=" N ILE B 483 " --> pdb=" O VAL B 534 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 577 through 580 removed outlier: 3.985A pdb=" N LYS B 577 " --> pdb=" O LYS B 624 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS B 590 " --> pdb=" O GLU B 627 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 99 through 101 removed outlier: 6.817A pdb=" N ALA C 6 " --> pdb=" O SER C 100 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU C 74 " --> pdb=" O LYS C 67 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 28 through 31 removed outlier: 4.123A pdb=" N PHE C 47 " --> pdb=" O GLY C 42 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 99 through 101 removed outlier: 6.250A pdb=" N ALA D 6 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 28 through 31 removed outlier: 3.504A pdb=" N HIS D 49 " --> pdb=" O CYS D 40 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY D 42 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE D 47 " --> pdb=" O GLY D 42 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 291 through 294 removed outlier: 6.307A pdb=" N LYS E 284 " --> pdb=" O ILE E 292 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N CYS E 294 " --> pdb=" O ARG E 282 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ARG E 282 " --> pdb=" O CYS E 294 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE E 364 " --> pdb=" O ASP E 371 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE E 373 " --> pdb=" O ARG E 362 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ARG E 362 " --> pdb=" O ILE E 373 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA E 375 " --> pdb=" O ASN E 360 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASN E 360 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N GLN E 377 " --> pdb=" O GLN E 358 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLN E 358 " --> pdb=" O GLN E 377 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N TRP E 356 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG E 355 " --> pdb=" O LEU E 347 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 39 through 41 Processing sheet with id= O, first strand: chain 'F' and resid 34 through 36 removed outlier: 3.646A pdb=" N THR F 35 " --> pdb=" O LYS F 156 " (cutoff:3.500A) 549 hydrogen bonds defined for protein. 1488 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.71 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2702 1.32 - 1.44: 4056 1.44 - 1.57: 9132 1.57 - 1.69: 8 1.69 - 1.82: 121 Bond restraints: 16019 Sorted by residual: bond pdb=" CA ASP D 70 " pdb=" C ASP D 70 " ideal model delta sigma weight residual 1.520 1.421 0.099 1.25e-02 6.40e+03 6.29e+01 bond pdb=" CA ASP B 672 " pdb=" C ASP B 672 " ideal model delta sigma weight residual 1.531 1.572 -0.040 7.40e-03 1.83e+04 2.97e+01 bond pdb=" N ARG D 71 " pdb=" CA ARG D 71 " ideal model delta sigma weight residual 1.458 1.389 0.069 1.33e-02 5.65e+03 2.66e+01 bond pdb=" CA THR C 69 " pdb=" C THR C 69 " ideal model delta sigma weight residual 1.526 1.459 0.067 1.37e-02 5.33e+03 2.40e+01 bond pdb=" BE BEF A 802 " pdb=" F2 BEF A 802 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.83e+01 ... (remaining 16014 not shown) Histogram of bond angle deviations from ideal: 96.49 - 104.42: 209 104.42 - 112.36: 7972 112.36 - 120.29: 6960 120.29 - 128.22: 6309 128.22 - 136.16: 114 Bond angle restraints: 21564 Sorted by residual: angle pdb=" C LYS D 65 " pdb=" CA LYS D 65 " pdb=" CB LYS D 65 " ideal model delta sigma weight residual 110.62 100.83 9.79 1.86e+00 2.89e-01 2.77e+01 angle pdb=" N LEU E 325 " pdb=" CA LEU E 325 " pdb=" C LEU E 325 " ideal model delta sigma weight residual 112.89 106.74 6.15 1.24e+00 6.50e-01 2.46e+01 angle pdb=" C1' ADP B 801 " pdb=" C2' ADP B 801 " pdb=" C3' ADP B 801 " ideal model delta sigma weight residual 111.00 96.59 14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" N TYR F 98 " pdb=" CA TYR F 98 " pdb=" C TYR F 98 " ideal model delta sigma weight residual 112.55 118.69 -6.14 1.35e+00 5.49e-01 2.07e+01 angle pdb=" N CYS E 327 " pdb=" CA CYS E 327 " pdb=" C CYS E 327 " ideal model delta sigma weight residual 112.90 107.20 5.70 1.31e+00 5.83e-01 1.90e+01 ... (remaining 21559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.16: 9462 31.16 - 62.33: 325 62.33 - 93.49: 28 93.49 - 124.65: 0 124.65 - 155.82: 3 Dihedral angle restraints: 9818 sinusoidal: 4156 harmonic: 5662 Sorted by residual: dihedral pdb=" O2A ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PA ADP A 801 " pdb=" PB ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 144.19 155.82 1 2.00e+01 2.50e-03 4.59e+01 dihedral pdb=" C5' ADP B 801 " pdb=" O5' ADP B 801 " pdb=" PA ADP B 801 " pdb=" O2A ADP B 801 " ideal model delta sinusoidal sigma weight residual -60.00 94.96 -154.96 1 2.00e+01 2.50e-03 4.57e+01 dihedral pdb=" C5' ADP A 801 " pdb=" O5' ADP A 801 " pdb=" PA ADP A 801 " pdb=" O2A ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 79.51 -139.51 1 2.00e+01 2.50e-03 4.23e+01 ... (remaining 9815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 2208 0.095 - 0.189: 139 0.189 - 0.284: 6 0.284 - 0.378: 1 0.378 - 0.473: 1 Chirality restraints: 2355 Sorted by residual: chirality pdb=" CA ILE E 374 " pdb=" N ILE E 374 " pdb=" C ILE E 374 " pdb=" CB ILE E 374 " both_signs ideal model delta sigma weight residual False 2.43 2.91 -0.47 2.00e-01 2.50e+01 5.58e+00 chirality pdb=" CA THR C 69 " pdb=" N THR C 69 " pdb=" C THR C 69 " pdb=" CB THR C 69 " both_signs ideal model delta sigma weight residual False 2.53 2.20 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" C2' ADP B 801 " pdb=" C1' ADP B 801 " pdb=" C3' ADP B 801 " pdb=" O2' ADP B 801 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 2352 not shown) Planarity restraints: 2764 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 78 " 0.047 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO B 79 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO B 79 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 79 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 396 " 0.033 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO E 397 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO E 397 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 397 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 285 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C HIS E 285 " 0.033 2.00e-02 2.50e+03 pdb=" O HIS E 285 " -0.012 2.00e-02 2.50e+03 pdb=" N LYS E 286 " -0.011 2.00e-02 2.50e+03 ... (remaining 2761 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 3 2.07 - 2.78: 3363 2.78 - 3.49: 21704 3.49 - 4.19: 35327 4.19 - 4.90: 61950 Nonbonded interactions: 122347 Sorted by model distance: nonbonded pdb=" OD1 ASN B 46 " pdb=" F1 BEF B 802 " model vdw 1.365 2.390 nonbonded pdb=" CE LYS E 286 " pdb=" CG2 ILE E 292 " model vdw 1.866 3.860 nonbonded pdb=" OG1 THR E 381 " pdb=" OE1 GLU E 384 " model vdw 2.063 2.440 nonbonded pdb=" NE2 GLN F 315 " pdb=" OE2 GLU F 319 " model vdw 2.096 2.520 nonbonded pdb=" O2' ADP B 801 " pdb=" O3' ADP B 801 " model vdw 2.106 2.432 ... (remaining 122342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 217 or resid 278 through 690 or resid 801 throu \ gh 802)) selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 1 through 111) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.290 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 42.010 Find NCS groups from input model: 1.020 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 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 : 0.005 0.099 16019 Z= 0.329 Angle : 0.839 14.411 21564 Z= 0.473 Chirality : 0.050 0.473 2355 Planarity : 0.004 0.069 2764 Dihedral : 15.363 155.815 6142 Min Nonbonded Distance : 1.365 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.12 % Allowed : 0.87 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.18), residues: 1912 helix: -0.22 (0.20), residues: 684 sheet: -0.39 (0.29), residues: 325 loop : -1.94 (0.18), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 109 HIS 0.017 0.002 HIS E 285 PHE 0.032 0.002 PHE E 289 TYR 0.019 0.002 TYR F 163 ARG 0.013 0.001 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 420 time to evaluate : 1.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7975 (ptmm) cc_final: 0.6983 (mmtt) REVERT: A 125 MET cc_start: 0.6936 (mtm) cc_final: 0.6710 (mtm) REVERT: A 288 ILE cc_start: 0.8391 (mt) cc_final: 0.8147 (mt) REVERT: A 414 GLU cc_start: 0.7098 (tt0) cc_final: 0.6859 (mt-10) REVERT: A 450 ARG cc_start: 0.7490 (ptp-110) cc_final: 0.7182 (ptp90) REVERT: A 492 GLU cc_start: 0.6980 (tp30) cc_final: 0.6711 (tp30) REVERT: A 515 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7858 (mm-30) REVERT: A 553 MET cc_start: 0.5302 (tpp) cc_final: 0.4963 (tpp) REVERT: A 576 GLU cc_start: 0.6321 (mm-30) cc_final: 0.5909 (tp30) REVERT: A 603 GLU cc_start: 0.6681 (tt0) cc_final: 0.6010 (tp30) REVERT: A 681 TYR cc_start: 0.7317 (m-10) cc_final: 0.7111 (m-10) REVERT: B 18 GLN cc_start: 0.7433 (mt0) cc_final: 0.7136 (tt0) REVERT: B 69 LYS cc_start: 0.7395 (ptpt) cc_final: 0.6692 (mmtt) REVERT: B 88 ASP cc_start: 0.6405 (p0) cc_final: 0.5967 (p0) REVERT: B 100 ASN cc_start: 0.7769 (t0) cc_final: 0.7413 (t0) REVERT: B 123 ILE cc_start: 0.6757 (mm) cc_final: 0.6516 (tt) REVERT: B 174 PRO cc_start: 0.8466 (Cg_endo) cc_final: 0.8244 (Cg_exo) REVERT: B 286 LYS cc_start: 0.8276 (mtmt) cc_final: 0.8022 (mttt) REVERT: B 344 PHE cc_start: 0.6001 (m-10) cc_final: 0.5753 (m-80) REVERT: B 424 GLU cc_start: 0.7270 (tm-30) cc_final: 0.7032 (mp0) REVERT: B 450 ARG cc_start: 0.7248 (ttm-80) cc_final: 0.6843 (ttp-170) REVERT: B 477 LYS cc_start: 0.7482 (mmmm) cc_final: 0.7111 (mtpt) REVERT: B 621 MET cc_start: 0.7528 (mmm) cc_final: 0.6934 (mmt) REVERT: B 637 THR cc_start: 0.7349 (m) cc_final: 0.7030 (t) REVERT: B 665 SER cc_start: 0.6905 (t) cc_final: 0.6618 (m) REVERT: C 7 LYS cc_start: 0.8016 (mttm) cc_final: 0.7552 (mttt) REVERT: C 104 ASN cc_start: 0.8169 (m110) cc_final: 0.7927 (m-40) REVERT: C 107 LYS cc_start: 0.7550 (ttmt) cc_final: 0.7029 (ttpp) REVERT: D 78 ARG cc_start: 0.6182 (ttm-80) cc_final: 0.5893 (ttt180) REVERT: E 270 SER cc_start: 0.8122 (m) cc_final: 0.7719 (p) REVERT: E 320 HIS cc_start: 0.6918 (t-90) cc_final: 0.6307 (t-90) REVERT: E 324 MET cc_start: 0.5796 (ptm) cc_final: 0.4251 (tpt) REVERT: E 334 MET cc_start: 0.6275 (ttp) cc_final: 0.5947 (ptp) REVERT: E 350 LYS cc_start: 0.4927 (pttm) cc_final: 0.3792 (tptp) REVERT: E 355 ARG cc_start: 0.6607 (mmt180) cc_final: 0.5962 (ttm-80) REVERT: E 358 GLN cc_start: 0.6872 (tp40) cc_final: 0.6655 (tt0) REVERT: E 363 LEU cc_start: 0.7260 (pt) cc_final: 0.6660 (tp) REVERT: E 364 ILE cc_start: 0.7010 (mm) cc_final: 0.6660 (mm) REVERT: E 383 GLU cc_start: 0.6846 (mp0) cc_final: 0.6520 (mp0) REVERT: F 153 GLU cc_start: 0.2646 (tt0) cc_final: 0.2202 (mt-10) REVERT: F 184 GLN cc_start: 0.6167 (tm-30) cc_final: 0.5871 (pt0) REVERT: F 203 TYR cc_start: 0.6105 (t80) cc_final: 0.5722 (t80) REVERT: F 214 MET cc_start: 0.7545 (mtm) cc_final: 0.7056 (ptp) REVERT: F 223 TRP cc_start: 0.6647 (t60) cc_final: 0.5843 (t60) outliers start: 2 outliers final: 0 residues processed: 421 average time/residue: 0.3368 time to fit residues: 195.0778 Evaluate side-chains 242 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 174 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 HIS ** E 299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 HIS E 351 HIS ** F 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16019 Z= 0.246 Angle : 0.649 8.396 21564 Z= 0.338 Chirality : 0.046 0.185 2355 Planarity : 0.004 0.049 2764 Dihedral : 7.202 132.207 2115 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.71 % Favored : 95.24 % Rotamer: Outliers : 2.02 % Allowed : 9.60 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.19), residues: 1912 helix: 0.02 (0.20), residues: 681 sheet: 0.10 (0.29), residues: 334 loop : -1.69 (0.19), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 157 HIS 0.011 0.001 HIS E 331 PHE 0.029 0.002 PHE E 345 TYR 0.021 0.002 TYR A 472 ARG 0.005 0.001 ARG C 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 273 time to evaluate : 2.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7890 (ptmm) cc_final: 0.6893 (mmtt) REVERT: A 366 CYS cc_start: 0.6623 (t) cc_final: 0.6341 (t) REVERT: A 414 GLU cc_start: 0.6755 (tt0) cc_final: 0.6546 (mt-10) REVERT: A 449 ARG cc_start: 0.6173 (tmm160) cc_final: 0.5967 (tmm160) REVERT: A 450 ARG cc_start: 0.7501 (ptp-110) cc_final: 0.6905 (ptp90) REVERT: A 509 GLU cc_start: 0.6606 (pm20) cc_final: 0.6369 (pm20) REVERT: A 515 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 553 MET cc_start: 0.5228 (tpp) cc_final: 0.5009 (tpp) REVERT: A 576 GLU cc_start: 0.6364 (mm-30) cc_final: 0.5863 (tp30) REVERT: A 637 THR cc_start: 0.7854 (m) cc_final: 0.7537 (p) REVERT: A 682 ARG cc_start: 0.6972 (tpt170) cc_final: 0.6713 (tpt170) REVERT: B 25 MET cc_start: 0.7152 (tpp) cc_final: 0.6873 (tpp) REVERT: B 100 ASN cc_start: 0.7779 (t0) cc_final: 0.7373 (t0) REVERT: B 123 ILE cc_start: 0.6775 (mm) cc_final: 0.6391 (tt) REVERT: B 174 PRO cc_start: 0.8533 (Cg_endo) cc_final: 0.8295 (Cg_exo) REVERT: B 286 LYS cc_start: 0.8378 (mtmt) cc_final: 0.8125 (mttt) REVERT: B 368 GLU cc_start: 0.6563 (mt-10) cc_final: 0.5810 (mp0) REVERT: B 424 GLU cc_start: 0.7282 (tm-30) cc_final: 0.7059 (mp0) REVERT: B 450 ARG cc_start: 0.7313 (ttm-80) cc_final: 0.6826 (ttp-170) REVERT: B 477 LYS cc_start: 0.7450 (mmmm) cc_final: 0.7082 (mtpt) REVERT: B 506 ARG cc_start: 0.6704 (mpt180) cc_final: 0.6487 (mpt180) REVERT: B 513 MET cc_start: 0.8173 (mtp) cc_final: 0.7968 (mtt) REVERT: B 621 MET cc_start: 0.7738 (mmm) cc_final: 0.6962 (mmt) REVERT: B 627 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: B 637 THR cc_start: 0.7413 (m) cc_final: 0.7018 (t) REVERT: C 7 LYS cc_start: 0.8016 (mttm) cc_final: 0.7544 (mttt) REVERT: C 104 ASN cc_start: 0.8235 (m110) cc_final: 0.7881 (m-40) REVERT: E 270 SER cc_start: 0.8071 (m) cc_final: 0.7755 (p) REVERT: E 282 ARG cc_start: 0.5058 (mtm-85) cc_final: 0.4336 (mtm180) REVERT: E 324 MET cc_start: 0.6061 (ptm) cc_final: 0.5044 (tpt) REVERT: E 350 LYS cc_start: 0.4876 (pttm) cc_final: 0.3726 (tptp) REVERT: E 399 MET cc_start: 0.4710 (ptt) cc_final: 0.4272 (ptm) REVERT: F 80 MET cc_start: 0.3533 (mtm) cc_final: 0.3248 (mtp) REVERT: F 153 GLU cc_start: 0.2688 (tt0) cc_final: 0.2234 (mt-10) REVERT: F 154 MET cc_start: 0.2539 (tpt) cc_final: 0.1765 (tpt) REVERT: F 184 GLN cc_start: 0.6282 (tm-30) cc_final: 0.5945 (pt0) REVERT: F 214 MET cc_start: 0.7574 (mtm) cc_final: 0.7036 (ptp) REVERT: F 252 ASP cc_start: 0.6566 (m-30) cc_final: 0.6192 (m-30) REVERT: F 265 VAL cc_start: 0.7088 (p) cc_final: 0.6824 (t) outliers start: 35 outliers final: 20 residues processed: 293 average time/residue: 0.3149 time to fit residues: 130.7024 Evaluate side-chains 250 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 229 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 627 GLU Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9980 chunk 54 optimal weight: 10.0000 chunk 145 optimal weight: 0.0060 chunk 118 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 174 optimal weight: 5.9990 chunk 188 optimal weight: 8.9990 chunk 155 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 140 optimal weight: 7.9990 overall best weight: 1.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 632 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN ** D 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 299 GLN F 146 GLN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16019 Z= 0.237 Angle : 0.612 7.797 21564 Z= 0.317 Chirality : 0.044 0.157 2355 Planarity : 0.004 0.049 2764 Dihedral : 6.688 124.976 2115 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.01 % Allowed : 12.60 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.19), residues: 1912 helix: 0.05 (0.20), residues: 699 sheet: 0.14 (0.29), residues: 339 loop : -1.59 (0.19), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 157 HIS 0.005 0.001 HIS A 149 PHE 0.029 0.002 PHE E 345 TYR 0.014 0.002 TYR A 472 ARG 0.004 0.000 ARG B 612 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 237 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6054 (OUTLIER) cc_final: 0.5761 (tt) REVERT: A 204 LYS cc_start: 0.8307 (ttpt) cc_final: 0.7900 (tttp) REVERT: A 366 CYS cc_start: 0.6170 (t) cc_final: 0.5924 (t) REVERT: A 450 ARG cc_start: 0.7495 (ptp-110) cc_final: 0.7061 (ptp90) REVERT: A 515 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7893 (mm-30) REVERT: A 576 GLU cc_start: 0.6434 (mm-30) cc_final: 0.5821 (tp30) REVERT: A 637 THR cc_start: 0.7972 (m) cc_final: 0.7610 (p) REVERT: B 25 MET cc_start: 0.7165 (tpp) cc_final: 0.6876 (tpp) REVERT: B 100 ASN cc_start: 0.7779 (t0) cc_final: 0.7388 (t0) REVERT: B 144 VAL cc_start: 0.7179 (OUTLIER) cc_final: 0.6713 (t) REVERT: B 284 LYS cc_start: 0.7101 (mtpt) cc_final: 0.6797 (mmtp) REVERT: B 286 LYS cc_start: 0.8430 (mtmt) cc_final: 0.8146 (mttt) REVERT: B 368 GLU cc_start: 0.6614 (mt-10) cc_final: 0.5930 (mp0) REVERT: B 424 GLU cc_start: 0.7364 (tm-30) cc_final: 0.7105 (mp0) REVERT: B 450 ARG cc_start: 0.7324 (ttm-80) cc_final: 0.6797 (ttp-170) REVERT: B 477 LYS cc_start: 0.7399 (mmmm) cc_final: 0.7041 (mtpt) REVERT: B 505 LYS cc_start: 0.7218 (mmmm) cc_final: 0.6833 (ttmm) REVERT: B 506 ARG cc_start: 0.6716 (mpt180) cc_final: 0.6402 (mpt180) REVERT: B 621 MET cc_start: 0.7791 (mmm) cc_final: 0.7423 (mmt) REVERT: B 637 THR cc_start: 0.7361 (m) cc_final: 0.6945 (t) REVERT: C 28 ASN cc_start: 0.7238 (t0) cc_final: 0.6849 (m-40) REVERT: C 104 ASN cc_start: 0.8151 (m110) cc_final: 0.7866 (m-40) REVERT: D 22 GLU cc_start: 0.6631 (mp0) cc_final: 0.6126 (mm-30) REVERT: E 270 SER cc_start: 0.7987 (m) cc_final: 0.7668 (p) REVERT: E 282 ARG cc_start: 0.5022 (mtm-85) cc_final: 0.4384 (mtm180) REVERT: E 299 GLN cc_start: 0.6262 (OUTLIER) cc_final: 0.5819 (mm-40) REVERT: E 324 MET cc_start: 0.5770 (ptm) cc_final: 0.4883 (tpt) REVERT: E 350 LYS cc_start: 0.4806 (pttm) cc_final: 0.3731 (tptp) REVERT: F 184 GLN cc_start: 0.6345 (tm-30) cc_final: 0.5956 (pt0) REVERT: F 214 MET cc_start: 0.7477 (mtm) cc_final: 0.7052 (ptp) REVERT: F 265 VAL cc_start: 0.7055 (p) cc_final: 0.6792 (t) outliers start: 52 outliers final: 37 residues processed: 273 average time/residue: 0.3126 time to fit residues: 121.0522 Evaluate side-chains 251 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 211 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 299 GLN Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 172 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 90 optimal weight: 0.0270 chunk 19 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 185 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 166 optimal weight: 0.4980 chunk 50 optimal weight: 0.7980 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN E 299 GLN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16019 Z= 0.181 Angle : 0.567 7.453 21564 Z= 0.293 Chirality : 0.042 0.165 2355 Planarity : 0.004 0.048 2764 Dihedral : 6.341 120.100 2115 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.01 % Allowed : 14.68 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1912 helix: 0.15 (0.20), residues: 703 sheet: 0.28 (0.29), residues: 318 loop : -1.48 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 157 HIS 0.005 0.001 HIS E 331 PHE 0.026 0.001 PHE E 345 TYR 0.012 0.001 TYR B 485 ARG 0.005 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 232 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LYS cc_start: 0.7838 (ptmm) cc_final: 0.6884 (mmtt) REVERT: A 86 LEU cc_start: 0.6073 (OUTLIER) cc_final: 0.5738 (tt) REVERT: A 204 LYS cc_start: 0.8304 (ttpt) cc_final: 0.7889 (tttp) REVERT: A 342 ASP cc_start: 0.6887 (OUTLIER) cc_final: 0.6655 (p0) REVERT: A 515 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7883 (mm-30) REVERT: A 637 THR cc_start: 0.7890 (m) cc_final: 0.7540 (p) REVERT: B 25 MET cc_start: 0.7148 (tpp) cc_final: 0.6884 (tpp) REVERT: B 144 VAL cc_start: 0.7173 (OUTLIER) cc_final: 0.6784 (t) REVERT: B 153 GLU cc_start: 0.7484 (tp30) cc_final: 0.6983 (mp0) REVERT: B 168 ARG cc_start: 0.6843 (mtp85) cc_final: 0.6485 (mtp85) REVERT: B 284 LYS cc_start: 0.7139 (mtpt) cc_final: 0.6670 (mmtm) REVERT: B 368 GLU cc_start: 0.6448 (mt-10) cc_final: 0.5803 (mp0) REVERT: B 450 ARG cc_start: 0.7319 (ttm-80) cc_final: 0.6758 (ttp-170) REVERT: B 477 LYS cc_start: 0.7377 (mmmm) cc_final: 0.7030 (mtpt) REVERT: B 505 LYS cc_start: 0.7252 (mmmm) cc_final: 0.6892 (ttmm) REVERT: B 637 THR cc_start: 0.7318 (m) cc_final: 0.6693 (t) REVERT: C 28 ASN cc_start: 0.7223 (t0) cc_final: 0.6857 (m-40) REVERT: C 104 ASN cc_start: 0.8147 (m110) cc_final: 0.7901 (m-40) REVERT: E 270 SER cc_start: 0.7908 (m) cc_final: 0.7535 (p) REVERT: E 282 ARG cc_start: 0.4896 (mtm-85) cc_final: 0.4369 (mtm180) REVERT: E 284 LYS cc_start: 0.6633 (ptpp) cc_final: 0.6384 (ptpp) REVERT: E 304 TYR cc_start: 0.5137 (OUTLIER) cc_final: 0.3614 (t80) REVERT: E 324 MET cc_start: 0.5665 (ptm) cc_final: 0.5047 (tpt) REVERT: E 333 ARG cc_start: 0.7139 (mtm110) cc_final: 0.6907 (ttp-170) REVERT: E 350 LYS cc_start: 0.4826 (pttm) cc_final: 0.3800 (tptp) REVERT: F 214 MET cc_start: 0.7453 (mtm) cc_final: 0.7032 (ptp) REVERT: F 265 VAL cc_start: 0.7096 (OUTLIER) cc_final: 0.6806 (t) REVERT: F 294 LEU cc_start: 0.6876 (mm) cc_final: 0.6275 (mm) outliers start: 52 outliers final: 38 residues processed: 266 average time/residue: 0.3095 time to fit residues: 117.2396 Evaluate side-chains 260 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 217 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 144 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Chi-restraints excluded: chain F residue 265 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 154 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 166 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 461 GLN D 97 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16019 Z= 0.367 Angle : 0.698 9.201 21564 Z= 0.360 Chirality : 0.048 0.220 2355 Planarity : 0.005 0.049 2764 Dihedral : 7.226 141.579 2115 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 3.82 % Allowed : 15.95 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 1912 helix: -0.06 (0.20), residues: 692 sheet: 0.06 (0.29), residues: 324 loop : -1.54 (0.19), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 157 HIS 0.007 0.002 HIS E 285 PHE 0.032 0.002 PHE E 345 TYR 0.020 0.002 TYR A 472 ARG 0.005 0.001 ARG E 312 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 217 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8284 (ttpt) cc_final: 0.7872 (tttp) REVERT: A 431 GLU cc_start: 0.6996 (pp20) cc_final: 0.6706 (tm-30) REVERT: A 515 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 523 GLN cc_start: 0.7293 (mm-40) cc_final: 0.6861 (mp10) REVERT: A 567 MET cc_start: 0.6057 (mmm) cc_final: 0.5378 (mmm) REVERT: A 576 GLU cc_start: 0.6269 (mt-10) cc_final: 0.5551 (tt0) REVERT: A 660 GLU cc_start: 0.7277 (mm-30) cc_final: 0.6947 (mm-30) REVERT: B 284 LYS cc_start: 0.7195 (mtpt) cc_final: 0.6705 (mmtm) REVERT: B 368 GLU cc_start: 0.6284 (mt-10) cc_final: 0.5628 (mp0) REVERT: B 402 LYS cc_start: 0.6652 (ttmt) cc_final: 0.6211 (tttp) REVERT: B 450 ARG cc_start: 0.7453 (ttm-80) cc_final: 0.6951 (ttp-170) REVERT: B 477 LYS cc_start: 0.7423 (mmmm) cc_final: 0.7011 (mtpt) REVERT: B 480 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7026 (tt0) REVERT: B 489 GLU cc_start: 0.6289 (pt0) cc_final: 0.6070 (tp30) REVERT: B 620 MET cc_start: 0.6876 (mpp) cc_final: 0.5657 (mpp) REVERT: B 637 THR cc_start: 0.7253 (m) cc_final: 0.6829 (t) REVERT: B 658 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7634 (mt) REVERT: C 28 ASN cc_start: 0.7430 (t0) cc_final: 0.7027 (m110) REVERT: D 22 GLU cc_start: 0.6855 (mp0) cc_final: 0.6369 (mm-30) REVERT: D 70 ASP cc_start: 0.7801 (t0) cc_final: 0.7125 (m-30) REVERT: D 105 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7565 (p0) REVERT: E 270 SER cc_start: 0.8022 (m) cc_final: 0.7602 (p) REVERT: E 282 ARG cc_start: 0.5144 (mtm-85) cc_final: 0.4422 (mtm180) REVERT: E 284 LYS cc_start: 0.6656 (ptpp) cc_final: 0.6364 (ptpp) REVERT: E 304 TYR cc_start: 0.5146 (OUTLIER) cc_final: 0.3514 (t80) REVERT: E 324 MET cc_start: 0.6001 (ptm) cc_final: 0.5325 (tpt) REVERT: E 333 ARG cc_start: 0.7103 (mtm110) cc_final: 0.6854 (mtm110) REVERT: E 350 LYS cc_start: 0.4552 (pttm) cc_final: 0.3589 (tptp) REVERT: F 194 GLN cc_start: 0.4801 (mm110) cc_final: 0.4374 (mm110) REVERT: F 214 MET cc_start: 0.7474 (mtm) cc_final: 0.7045 (ptp) REVERT: F 261 TYR cc_start: 0.6114 (m-10) cc_final: 0.5794 (m-10) REVERT: F 265 VAL cc_start: 0.7108 (OUTLIER) cc_final: 0.6818 (t) REVERT: F 292 LEU cc_start: 0.5725 (OUTLIER) cc_final: 0.5486 (mm) outliers start: 66 outliers final: 50 residues processed: 268 average time/residue: 0.2878 time to fit residues: 111.5783 Evaluate side-chains 256 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 200 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 281 GLU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 480 GLN Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 602 MET Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 82 GLU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 292 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 62 optimal weight: 4.9990 chunk 167 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 185 optimal weight: 8.9990 chunk 154 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6571 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16019 Z= 0.205 Angle : 0.585 8.943 21564 Z= 0.301 Chirality : 0.043 0.164 2355 Planarity : 0.004 0.048 2764 Dihedral : 6.553 129.006 2115 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.41 % Allowed : 17.51 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.19), residues: 1912 helix: 0.08 (0.20), residues: 698 sheet: 0.15 (0.29), residues: 315 loop : -1.46 (0.19), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 157 HIS 0.008 0.001 HIS E 285 PHE 0.026 0.001 PHE E 345 TYR 0.017 0.001 TYR A 472 ARG 0.002 0.000 ARG F 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 222 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6108 (OUTLIER) cc_final: 0.5789 (tt) REVERT: A 204 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7854 (tttp) REVERT: A 279 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.6341 (mm110) REVERT: A 342 ASP cc_start: 0.6956 (OUTLIER) cc_final: 0.6723 (p0) REVERT: A 431 GLU cc_start: 0.6990 (pp20) cc_final: 0.6762 (tm-30) REVERT: A 515 GLU cc_start: 0.8281 (mm-30) cc_final: 0.7404 (mm-30) REVERT: A 576 GLU cc_start: 0.5924 (mt-10) cc_final: 0.5286 (tt0) REVERT: A 660 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7085 (mm-30) REVERT: B 153 GLU cc_start: 0.7545 (tp30) cc_final: 0.7090 (mp0) REVERT: B 168 ARG cc_start: 0.6751 (mtp85) cc_final: 0.6402 (mtt-85) REVERT: B 284 LYS cc_start: 0.7242 (mtpt) cc_final: 0.6754 (mmtm) REVERT: B 368 GLU cc_start: 0.6258 (mt-10) cc_final: 0.5583 (mp0) REVERT: B 397 GLN cc_start: 0.7962 (mm110) cc_final: 0.7470 (mm110) REVERT: B 450 ARG cc_start: 0.7175 (ttm-80) cc_final: 0.6766 (ttp-170) REVERT: B 477 LYS cc_start: 0.7435 (mmmm) cc_final: 0.6916 (mtpt) REVERT: B 505 LYS cc_start: 0.7426 (mmmm) cc_final: 0.7061 (ttmm) REVERT: B 620 MET cc_start: 0.6879 (mpp) cc_final: 0.5685 (mpp) REVERT: B 637 THR cc_start: 0.7144 (m) cc_final: 0.6746 (t) REVERT: B 658 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7674 (mt) REVERT: C 7 LYS cc_start: 0.8103 (mttm) cc_final: 0.7898 (mmtp) REVERT: C 28 ASN cc_start: 0.7427 (t0) cc_final: 0.7059 (m110) REVERT: D 22 GLU cc_start: 0.6879 (mp0) cc_final: 0.6510 (mm-30) REVERT: D 70 ASP cc_start: 0.7788 (t0) cc_final: 0.7138 (m-30) REVERT: D 105 ASN cc_start: 0.8073 (OUTLIER) cc_final: 0.7617 (p0) REVERT: E 270 SER cc_start: 0.7983 (m) cc_final: 0.7534 (p) REVERT: E 282 ARG cc_start: 0.4976 (mtm-85) cc_final: 0.4380 (mtm180) REVERT: E 304 TYR cc_start: 0.5114 (OUTLIER) cc_final: 0.3477 (t80) REVERT: E 318 PHE cc_start: 0.5474 (p90) cc_final: 0.5035 (m-80) REVERT: E 324 MET cc_start: 0.6036 (ptm) cc_final: 0.5354 (tpt) REVERT: E 350 LYS cc_start: 0.4549 (pttm) cc_final: 0.3635 (tptp) REVERT: F 194 GLN cc_start: 0.4719 (mm110) cc_final: 0.4279 (mm110) REVERT: F 214 MET cc_start: 0.7416 (mtm) cc_final: 0.7002 (ptp) REVERT: F 265 VAL cc_start: 0.7065 (OUTLIER) cc_final: 0.6788 (t) REVERT: F 292 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5521 (mm) outliers start: 59 outliers final: 37 residues processed: 263 average time/residue: 0.3046 time to fit residues: 114.1267 Evaluate side-chains 258 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 213 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain D residue 105 ASN Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 292 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 0.0470 chunk 185 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 85 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6551 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16019 Z= 0.168 Angle : 0.562 8.988 21564 Z= 0.288 Chirality : 0.042 0.216 2355 Planarity : 0.004 0.048 2764 Dihedral : 6.254 122.213 2115 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 3.12 % Allowed : 17.98 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.19), residues: 1912 helix: 0.17 (0.20), residues: 704 sheet: 0.19 (0.30), residues: 320 loop : -1.35 (0.20), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 157 HIS 0.008 0.001 HIS E 285 PHE 0.024 0.001 PHE E 345 TYR 0.012 0.001 TYR A 472 ARG 0.008 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 220 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6139 (OUTLIER) cc_final: 0.5751 (tt) REVERT: A 204 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7859 (tttp) REVERT: A 279 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.6333 (mm110) REVERT: A 342 ASP cc_start: 0.7051 (OUTLIER) cc_final: 0.6806 (p0) REVERT: A 431 GLU cc_start: 0.6996 (pp20) cc_final: 0.6750 (tm-30) REVERT: A 504 ARG cc_start: 0.7203 (mtm110) cc_final: 0.6922 (mtp180) REVERT: A 515 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7500 (mm-30) REVERT: B 153 GLU cc_start: 0.7493 (tp30) cc_final: 0.7059 (mp0) REVERT: B 168 ARG cc_start: 0.6828 (mtp85) cc_final: 0.6402 (mtt-85) REVERT: B 284 LYS cc_start: 0.7243 (mtpt) cc_final: 0.6762 (mmtm) REVERT: B 288 ILE cc_start: 0.7690 (pt) cc_final: 0.7474 (mt) REVERT: B 368 GLU cc_start: 0.6243 (mt-10) cc_final: 0.5573 (mp0) REVERT: B 397 GLN cc_start: 0.7837 (mm110) cc_final: 0.7331 (mm110) REVERT: B 450 ARG cc_start: 0.7161 (ttm-80) cc_final: 0.6772 (ttp-170) REVERT: B 477 LYS cc_start: 0.7376 (mmmm) cc_final: 0.6874 (mtpt) REVERT: B 620 MET cc_start: 0.6869 (mpp) cc_final: 0.5695 (mpp) REVERT: B 637 THR cc_start: 0.7101 (m) cc_final: 0.6713 (t) REVERT: B 658 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7693 (mt) REVERT: C 7 LYS cc_start: 0.8109 (mttm) cc_final: 0.7765 (mmtp) REVERT: C 28 ASN cc_start: 0.7339 (t0) cc_final: 0.7002 (m110) REVERT: D 22 GLU cc_start: 0.6872 (mp0) cc_final: 0.6516 (mm-30) REVERT: D 70 ASP cc_start: 0.7782 (t0) cc_final: 0.7177 (m-30) REVERT: E 270 SER cc_start: 0.7912 (m) cc_final: 0.7484 (p) REVERT: E 282 ARG cc_start: 0.4837 (mtm-85) cc_final: 0.4331 (mtm180) REVERT: E 304 TYR cc_start: 0.5061 (OUTLIER) cc_final: 0.3454 (t80) REVERT: E 324 MET cc_start: 0.6074 (ptm) cc_final: 0.5321 (tpt) REVERT: E 350 LYS cc_start: 0.4494 (pttm) cc_final: 0.3588 (tptp) REVERT: F 101 VAL cc_start: 0.0646 (OUTLIER) cc_final: 0.0384 (m) REVERT: F 194 GLN cc_start: 0.4699 (mm110) cc_final: 0.4271 (mm110) REVERT: F 214 MET cc_start: 0.7377 (mtm) cc_final: 0.6982 (ptp) REVERT: F 265 VAL cc_start: 0.7183 (OUTLIER) cc_final: 0.6922 (t) REVERT: F 294 LEU cc_start: 0.6745 (OUTLIER) cc_final: 0.6060 (mm) outliers start: 54 outliers final: 38 residues processed: 259 average time/residue: 0.3107 time to fit residues: 115.3008 Evaluate side-chains 255 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 209 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 294 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 117 optimal weight: 0.3980 chunk 126 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16019 Z= 0.232 Angle : 0.597 9.898 21564 Z= 0.306 Chirality : 0.043 0.206 2355 Planarity : 0.004 0.046 2764 Dihedral : 6.410 126.015 2115 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.12 % Allowed : 18.55 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.19), residues: 1912 helix: 0.13 (0.20), residues: 706 sheet: 0.17 (0.30), residues: 320 loop : -1.35 (0.20), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 157 HIS 0.009 0.001 HIS E 285 PHE 0.026 0.001 PHE E 345 TYR 0.012 0.002 TYR A 472 ARG 0.006 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 207 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 204 LYS cc_start: 0.8271 (ttpt) cc_final: 0.7866 (tttp) REVERT: A 279 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6387 (mm110) REVERT: A 342 ASP cc_start: 0.7036 (OUTLIER) cc_final: 0.6806 (p0) REVERT: A 431 GLU cc_start: 0.7006 (pp20) cc_final: 0.6693 (tm-30) REVERT: A 504 ARG cc_start: 0.7263 (mtm110) cc_final: 0.6945 (mtp180) REVERT: B 153 GLU cc_start: 0.7510 (tp30) cc_final: 0.7126 (mp0) REVERT: B 168 ARG cc_start: 0.6843 (mtp85) cc_final: 0.6404 (mtt-85) REVERT: B 284 LYS cc_start: 0.7213 (mtpt) cc_final: 0.6735 (mmtm) REVERT: B 368 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5583 (mp0) REVERT: B 397 GLN cc_start: 0.7838 (mm110) cc_final: 0.7315 (mm110) REVERT: B 450 ARG cc_start: 0.7121 (ttm-80) cc_final: 0.6738 (ttp-170) REVERT: B 477 LYS cc_start: 0.7372 (mmmm) cc_final: 0.6879 (mtpt) REVERT: B 620 MET cc_start: 0.6837 (mpp) cc_final: 0.5670 (mpp) REVERT: B 637 THR cc_start: 0.7106 (m) cc_final: 0.6717 (t) REVERT: B 658 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7685 (mt) REVERT: C 7 LYS cc_start: 0.8055 (mttm) cc_final: 0.7702 (mmtp) REVERT: C 28 ASN cc_start: 0.7345 (t0) cc_final: 0.6998 (m110) REVERT: D 22 GLU cc_start: 0.6868 (mp0) cc_final: 0.6511 (mm-30) REVERT: D 70 ASP cc_start: 0.7801 (t0) cc_final: 0.7201 (m-30) REVERT: E 270 SER cc_start: 0.7938 (m) cc_final: 0.7508 (p) REVERT: E 282 ARG cc_start: 0.4869 (mtm-85) cc_final: 0.4327 (mtm180) REVERT: E 304 TYR cc_start: 0.5076 (OUTLIER) cc_final: 0.3473 (t80) REVERT: E 306 GLU cc_start: 0.5388 (tp30) cc_final: 0.5185 (tp30) REVERT: E 324 MET cc_start: 0.6074 (ptm) cc_final: 0.5340 (tpt) REVERT: E 334 MET cc_start: 0.6502 (ptp) cc_final: 0.6169 (ptp) REVERT: E 350 LYS cc_start: 0.4489 (pttm) cc_final: 0.3573 (tptp) REVERT: F 101 VAL cc_start: 0.0881 (OUTLIER) cc_final: 0.0638 (m) REVERT: F 194 GLN cc_start: 0.4700 (mm110) cc_final: 0.4264 (mm110) REVERT: F 214 MET cc_start: 0.7379 (mtm) cc_final: 0.6985 (ptp) REVERT: F 265 VAL cc_start: 0.7174 (OUTLIER) cc_final: 0.6911 (t) REVERT: F 294 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6093 (mm) outliers start: 54 outliers final: 42 residues processed: 246 average time/residue: 0.3031 time to fit residues: 107.5259 Evaluate side-chains 250 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 201 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 313 GLU Chi-restraints excluded: chain A residue 314 ASP Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 593 THR Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 428 LYS Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 591 ILE Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain C residue 39 SER Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 343 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 18 ILE Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Chi-restraints excluded: chain F residue 265 VAL Chi-restraints excluded: chain F residue 294 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 177 optimal weight: 7.9990 chunk 161 optimal weight: 8.9990 chunk 172 optimal weight: 0.0980 chunk 103 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 135 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 155 optimal weight: 0.9980 chunk 163 optimal weight: 0.5980 chunk 171 optimal weight: 0.0980 chunk 113 optimal weight: 0.0670 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN D 104 ASN ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6514 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16019 Z= 0.141 Angle : 0.545 11.811 21564 Z= 0.277 Chirality : 0.041 0.186 2355 Planarity : 0.003 0.048 2764 Dihedral : 5.844 111.294 2115 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.54 % Allowed : 18.96 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1912 helix: 0.24 (0.20), residues: 713 sheet: 0.28 (0.30), residues: 321 loop : -1.23 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 157 HIS 0.008 0.001 HIS E 285 PHE 0.019 0.001 PHE E 345 TYR 0.011 0.001 TYR A 485 ARG 0.008 0.000 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 223 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6174 (OUTLIER) cc_final: 0.5864 (tt) REVERT: A 204 LYS cc_start: 0.8259 (ttpt) cc_final: 0.7853 (tttp) REVERT: A 342 ASP cc_start: 0.6864 (OUTLIER) cc_final: 0.6625 (p0) REVERT: A 414 GLU cc_start: 0.6480 (tt0) cc_final: 0.6186 (mt-10) REVERT: A 431 GLU cc_start: 0.6997 (pp20) cc_final: 0.6732 (tm-30) REVERT: A 504 ARG cc_start: 0.7089 (mtm110) cc_final: 0.6838 (mtp180) REVERT: A 637 THR cc_start: 0.7612 (m) cc_final: 0.7383 (p) REVERT: B 153 GLU cc_start: 0.7382 (tp30) cc_final: 0.7062 (mp0) REVERT: B 168 ARG cc_start: 0.6834 (mtp85) cc_final: 0.6373 (mtt-85) REVERT: B 368 GLU cc_start: 0.6204 (mt-10) cc_final: 0.5547 (mp0) REVERT: B 397 GLN cc_start: 0.7713 (mm110) cc_final: 0.7173 (mm110) REVERT: B 450 ARG cc_start: 0.7080 (ttm-80) cc_final: 0.6699 (ttp-170) REVERT: B 477 LYS cc_start: 0.7352 (mmmm) cc_final: 0.6876 (mtpt) REVERT: B 620 MET cc_start: 0.6876 (mpp) cc_final: 0.5692 (mpp) REVERT: B 637 THR cc_start: 0.7160 (m) cc_final: 0.6769 (t) REVERT: B 658 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7718 (mt) REVERT: C 7 LYS cc_start: 0.8098 (mttm) cc_final: 0.7748 (mmtp) REVERT: C 28 ASN cc_start: 0.7287 (t0) cc_final: 0.6961 (m110) REVERT: D 70 ASP cc_start: 0.7828 (t0) cc_final: 0.7045 (m-30) REVERT: E 270 SER cc_start: 0.7698 (m) cc_final: 0.7387 (p) REVERT: E 282 ARG cc_start: 0.4709 (mtm-85) cc_final: 0.4458 (mtm180) REVERT: E 304 TYR cc_start: 0.4985 (OUTLIER) cc_final: 0.3463 (t80) REVERT: E 306 GLU cc_start: 0.5277 (tp30) cc_final: 0.5076 (tp30) REVERT: E 324 MET cc_start: 0.5963 (ptm) cc_final: 0.5275 (tpt) REVERT: E 333 ARG cc_start: 0.7124 (mtm110) cc_final: 0.6872 (ttp-170) REVERT: E 350 LYS cc_start: 0.4387 (pttm) cc_final: 0.3483 (tptp) REVERT: F 101 VAL cc_start: 0.0780 (OUTLIER) cc_final: 0.0485 (m) REVERT: F 194 GLN cc_start: 0.4527 (mm110) cc_final: 0.4137 (mm110) REVERT: F 214 MET cc_start: 0.7249 (mtm) cc_final: 0.6948 (ptp) REVERT: F 294 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6045 (mm) outliers start: 44 outliers final: 30 residues processed: 255 average time/residue: 0.3074 time to fit residues: 113.1370 Evaluate side-chains 243 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 207 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 25 MET Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 586 SER Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Chi-restraints excluded: chain F residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 182 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 0.0980 chunk 191 optimal weight: 0.7980 chunk 176 optimal weight: 3.9990 chunk 152 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16019 Z= 0.245 Angle : 0.611 11.786 21564 Z= 0.311 Chirality : 0.044 0.219 2355 Planarity : 0.004 0.047 2764 Dihedral : 6.284 120.551 2115 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.37 % Allowed : 19.25 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.19), residues: 1912 helix: 0.21 (0.20), residues: 708 sheet: 0.20 (0.30), residues: 320 loop : -1.19 (0.20), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 157 HIS 0.009 0.001 HIS E 285 PHE 0.023 0.002 PHE E 345 TYR 0.021 0.002 TYR A 681 ARG 0.006 0.000 ARG E 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3824 Ramachandran restraints generated. 1912 Oldfield, 0 Emsley, 1912 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 2.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5784 (tt) REVERT: A 204 LYS cc_start: 0.8269 (ttpt) cc_final: 0.7863 (tttp) REVERT: A 279 GLN cc_start: 0.7481 (OUTLIER) cc_final: 0.6401 (mm110) REVERT: A 342 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6747 (p0) REVERT: A 431 GLU cc_start: 0.7072 (pp20) cc_final: 0.6743 (tm-30) REVERT: A 523 GLN cc_start: 0.7168 (mm-40) cc_final: 0.6794 (mp10) REVERT: B 153 GLU cc_start: 0.7507 (tp30) cc_final: 0.7169 (mp0) REVERT: B 168 ARG cc_start: 0.6825 (mtp85) cc_final: 0.6380 (mtt-85) REVERT: B 368 GLU cc_start: 0.6186 (mt-10) cc_final: 0.5522 (mp0) REVERT: B 397 GLN cc_start: 0.7749 (mm110) cc_final: 0.7218 (mm110) REVERT: B 450 ARG cc_start: 0.7141 (ttm-80) cc_final: 0.6794 (ttp-170) REVERT: B 477 LYS cc_start: 0.7306 (mmmm) cc_final: 0.6929 (mtpt) REVERT: B 620 MET cc_start: 0.6824 (mpp) cc_final: 0.5644 (mpp) REVERT: B 637 THR cc_start: 0.7221 (m) cc_final: 0.6848 (t) REVERT: B 658 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7761 (mt) REVERT: C 7 LYS cc_start: 0.8108 (mttm) cc_final: 0.7763 (mmtp) REVERT: C 28 ASN cc_start: 0.7318 (t0) cc_final: 0.6992 (m110) REVERT: C 57 HIS cc_start: 0.7981 (m90) cc_final: 0.7676 (m-70) REVERT: D 22 GLU cc_start: 0.6854 (mp0) cc_final: 0.6487 (mm-30) REVERT: D 70 ASP cc_start: 0.7780 (t0) cc_final: 0.7065 (m-30) REVERT: E 270 SER cc_start: 0.7816 (m) cc_final: 0.7455 (p) REVERT: E 282 ARG cc_start: 0.4988 (mtm-85) cc_final: 0.4426 (mtm180) REVERT: E 304 TYR cc_start: 0.4940 (OUTLIER) cc_final: 0.3385 (t80) REVERT: E 324 MET cc_start: 0.6056 (ptm) cc_final: 0.5386 (tpt) REVERT: E 333 ARG cc_start: 0.7090 (mtm110) cc_final: 0.6813 (ttp-110) REVERT: E 350 LYS cc_start: 0.4399 (pttm) cc_final: 0.3470 (tptp) REVERT: F 101 VAL cc_start: 0.1020 (OUTLIER) cc_final: 0.0735 (m) REVERT: F 187 ASN cc_start: 0.5196 (m-40) cc_final: 0.4992 (m-40) REVERT: F 194 GLN cc_start: 0.4700 (mm110) cc_final: 0.4264 (mm110) REVERT: F 214 MET cc_start: 0.7380 (mtm) cc_final: 0.7044 (ptp) REVERT: F 294 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6053 (mm) outliers start: 41 outliers final: 31 residues processed: 238 average time/residue: 0.3196 time to fit residues: 110.4137 Evaluate side-chains 241 residues out of total 1730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 203 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 61 ASP Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 144 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 279 GLN Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 605 ILE Chi-restraints excluded: chain B residue 17 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 394 MET Chi-restraints excluded: chain B residue 468 SER Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 574 LYS Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 658 LEU Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 58 CYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 101 VAL Chi-restraints excluded: chain E residue 304 TYR Chi-restraints excluded: chain E residue 305 THR Chi-restraints excluded: chain E residue 345 PHE Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 391 LYS Chi-restraints excluded: chain E residue 402 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 238 CYS Chi-restraints excluded: chain F residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 140 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 42 optimal weight: 0.0030 chunk 152 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 133 optimal weight: 0.2980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.198187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.160078 restraints weight = 19386.833| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 1.85 r_work: 0.3665 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16019 Z= 0.152 Angle : 0.561 12.413 21564 Z= 0.285 Chirality : 0.041 0.182 2355 Planarity : 0.003 0.048 2764 Dihedral : 5.841 107.731 2115 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.31 % Allowed : 19.42 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.19), residues: 1912 helix: 0.27 (0.20), residues: 713 sheet: 0.27 (0.30), residues: 328 loop : -1.10 (0.20), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 157 HIS 0.009 0.001 HIS E 285 PHE 0.017 0.001 PHE E 345 TYR 0.018 0.001 TYR A 681 ARG 0.006 0.000 ARG E 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3594.78 seconds wall clock time: 65 minutes 24.95 seconds (3924.95 seconds total)