Starting phenix.real_space_refine on Mon Mar 11 08:58:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/03_2024/5u1d_8482.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/03_2024/5u1d_8482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/03_2024/5u1d_8482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/03_2024/5u1d_8482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/03_2024/5u1d_8482.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/03_2024/5u1d_8482.pdb" } resolution = 3.97 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= 0.036 sd= 0.252 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: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4900 2.51 5 N 1426 2.21 5 O 1458 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 312": "NH1" <-> "NH2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "X GLU 6": "OE1" <-> "OE2" Residue "X ARG 20": "NH1" <-> "NH2" Residue "X ARG 41": "NH1" <-> "NH2" Residue "X ARG 53": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7815 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 3635 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 18, 'TRANS': 542} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 744 Unresolved non-hydrogen angles: 962 Unresolved non-hydrogen dihedrals: 594 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 26, 'ASP:plan': 9, 'TYR:plan': 8, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 411 Chain: "B" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 3732 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 20, 'TRANS': 531} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 612 Unresolved non-hydrogen angles: 790 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 327 Chain: "X" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 448 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG A 529 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG A 529 " occ=0.50 residue: pdb=" N ARG B 494 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG B 494 " occ=0.50 Time building chain proxies: 4.79, per 1000 atoms: 0.61 Number of scatterers: 7815 At special positions: 0 Unit cell: (92.8618, 120.53, 116.905, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 31 16.00 O 1458 8.00 N 1426 7.00 C 4900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 1.7 seconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 73.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 185 through 202 removed outlier: 4.083A pdb=" N GLY A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.637A pdb=" N PHE A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 271 removed outlier: 3.871A pdb=" N PHE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 removed outlier: 4.230A pdb=" N PHE A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 removed outlier: 4.009A pdb=" N ILE A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 320 removed outlier: 3.564A pdb=" N LEU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 373 removed outlier: 3.648A pdb=" N ILE A 333 " --> pdb=" O MET A 329 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 4.223A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix removed outlier: 4.023A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 352 " --> pdb=" O TRP A 348 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 353 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.659A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 437 removed outlier: 3.640A pdb=" N ALA A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 462 removed outlier: 3.809A pdb=" N VAL A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 483 removed outlier: 4.162A pdb=" N ARG A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.505A pdb=" N ALA A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.751A pdb=" N THR A 634 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 removed outlier: 4.055A pdb=" N ARG A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.662A pdb=" N VAL A 706 " --> pdb=" O HIS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.648A pdb=" N LYS B 143 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 167 removed outlier: 4.073A pdb=" N LEU B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 removed outlier: 4.414A pdb=" N HIS B 171 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 236 removed outlier: 3.678A pdb=" N GLY B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 4.134A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 289 removed outlier: 4.797A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 264 " --> pdb=" O MET B 260 " (cutoff:3.500A) Proline residue: B 265 - end of helix removed outlier: 3.549A pdb=" N ILE B 288 " --> pdb=" O PHE B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.791A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 338 removed outlier: 3.685A pdb=" N ALA B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 401 removed outlier: 3.538A pdb=" N GLN B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 366 " --> pdb=" O CYS B 362 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 433 removed outlier: 3.790A pdb=" N LEU B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 449 removed outlier: 3.896A pdb=" N ALA B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 518 Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 584 Processing helix chain 'B' and resid 585 through 592 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.529A pdb=" N ALA B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 646 removed outlier: 4.359A pdb=" N GLU B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B 643 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 654 removed outlier: 3.760A pdb=" N SER B 650 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 654 " --> pdb=" O ARG B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 669 Processing helix chain 'X' and resid 2 through 14 removed outlier: 3.883A pdb=" N GLU X 6 " --> pdb=" O SER X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 44 removed outlier: 3.845A pdb=" N ASP X 24 " --> pdb=" O ARG X 20 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL X 25 " --> pdb=" O THR X 21 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP X 27 " --> pdb=" O ALA X 23 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG X 41 " --> pdb=" O ARG X 37 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL X 44 " --> pdb=" O ALA X 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 527 removed outlier: 5.019A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 526 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLN A 506 " --> pdb=" O PHE A 526 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 533 through 535 removed outlier: 6.903A pdb=" N THR A 534 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A 664 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 714 through 716 removed outlier: 3.727A pdb=" N GLU A 722 " --> pdb=" O PHE A 714 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 716 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 486 through 489 removed outlier: 5.093A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 548 through 549 removed outlier: 6.559A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1707 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2692 1.34 - 1.46: 649 1.46 - 1.58: 4523 1.58 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 7919 Sorted by residual: bond pdb=" CA ILE A 204 " pdb=" CB ILE A 204 " ideal model delta sigma weight residual 1.534 1.565 -0.031 6.80e-03 2.16e+04 2.05e+01 bond pdb=" CA ILE A 204 " pdb=" C ILE A 204 " ideal model delta sigma weight residual 1.520 1.545 -0.025 8.80e-03 1.29e+04 8.27e+00 bond pdb=" N LEU A 335 " pdb=" CA LEU A 335 " ideal model delta sigma weight residual 1.462 1.484 -0.023 9.50e-03 1.11e+04 5.67e+00 bond pdb=" N GLY B 524 " pdb=" CA GLY B 524 " ideal model delta sigma weight residual 1.446 1.469 -0.023 9.50e-03 1.11e+04 5.62e+00 bond pdb=" N ASP B 130 " pdb=" CA ASP B 130 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.90e-02 2.77e+03 4.87e+00 ... (remaining 7914 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.74: 142 106.74 - 113.55: 4166 113.55 - 120.35: 3186 120.35 - 127.16: 3250 127.16 - 133.97: 50 Bond angle restraints: 10794 Sorted by residual: angle pdb=" C ASP B 624 " pdb=" N PRO B 625 " pdb=" CA PRO B 625 " ideal model delta sigma weight residual 120.11 130.50 -10.39 1.12e+00 7.97e-01 8.61e+01 angle pdb=" C SER A 688 " pdb=" N PRO A 689 " pdb=" CA PRO A 689 " ideal model delta sigma weight residual 119.05 129.31 -10.26 1.11e+00 8.12e-01 8.54e+01 angle pdb=" C LYS A 660 " pdb=" N PRO A 661 " pdb=" CA PRO A 661 " ideal model delta sigma weight residual 120.31 128.17 -7.86 9.80e-01 1.04e+00 6.44e+01 angle pdb=" C LEU A 569 " pdb=" N PRO A 570 " pdb=" CA PRO A 570 " ideal model delta sigma weight residual 119.28 127.08 -7.80 1.10e+00 8.26e-01 5.03e+01 angle pdb=" C THR A 495 " pdb=" N PRO A 496 " pdb=" CA PRO A 496 " ideal model delta sigma weight residual 119.84 128.32 -8.48 1.25e+00 6.40e-01 4.60e+01 ... (remaining 10789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 4369 15.80 - 31.60: 210 31.60 - 47.40: 79 47.40 - 63.20: 20 63.20 - 79.00: 1 Dihedral angle restraints: 4679 sinusoidal: 1333 harmonic: 3346 Sorted by residual: dihedral pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" N GLU A 183 " pdb=" CA GLU A 183 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU A 183 " pdb=" C GLU A 183 " pdb=" N THR A 184 " pdb=" CA THR A 184 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA THR A 184 " pdb=" C THR A 184 " pdb=" N ARG A 185 " pdb=" CA ARG A 185 " ideal model delta harmonic sigma weight residual 180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 837 0.038 - 0.076: 297 0.076 - 0.114: 117 0.114 - 0.152: 36 0.152 - 0.190: 14 Chirality restraints: 1301 Sorted by residual: chirality pdb=" CA HIS X 45 " pdb=" N HIS X 45 " pdb=" C HIS X 45 " pdb=" CB HIS X 45 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA ASP A 483 " pdb=" N ASP A 483 " pdb=" C ASP A 483 " pdb=" CB ASP A 483 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA ILE A 204 " pdb=" N ILE A 204 " pdb=" C ILE A 204 " pdb=" CB ILE A 204 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 1298 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 300 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO B 301 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 146 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO B 147 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 465 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 466 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " -0.019 5.00e-02 4.00e+02 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 3099 2.94 - 3.43: 8317 3.43 - 3.92: 12011 3.92 - 4.41: 12091 4.41 - 4.90: 21589 Nonbonded interactions: 57107 Sorted by model distance: nonbonded pdb=" O GLU A 183 " pdb=" OG1 THR A 184 " model vdw 2.452 2.440 nonbonded pdb=" O MET B 218 " pdb=" OG SER B 261 " model vdw 2.513 2.440 nonbonded pdb=" O ARG X 20 " pdb=" OG1 THR X 21 " model vdw 2.563 2.440 nonbonded pdb=" O SER B 255 " pdb=" OG1 THR B 258 " model vdw 2.571 2.440 nonbonded pdb=" O LEU A 360 " pdb=" OG SER A 363 " model vdw 2.582 2.440 ... (remaining 57102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.640 Check model and map are aligned: 0.130 Set scattering table: 0.060 Process input model: 25.380 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5049 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 7919 Z= 0.493 Angle : 1.173 10.391 10794 Z= 0.861 Chirality : 0.050 0.190 1301 Planarity : 0.003 0.046 1427 Dihedral : 12.049 78.999 2521 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer: Outliers : 0.84 % Allowed : 1.69 % Favored : 97.47 % 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: -2.16 (0.21), residues: 1158 helix: -0.58 (0.15), residues: 765 sheet: -4.63 (0.65), residues: 37 loop : -2.79 (0.29), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 214 HIS 0.002 0.001 HIS B 539 PHE 0.013 0.001 PHE B 240 TYR 0.014 0.001 TYR B 446 ARG 0.005 0.001 ARG B 483 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 363 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7526 (t60) cc_final: 0.7319 (t60) REVERT: A 304 SER cc_start: 0.8176 (t) cc_final: 0.7835 (p) REVERT: A 317 LEU cc_start: 0.8945 (mt) cc_final: 0.8468 (mt) REVERT: A 351 LEU cc_start: 0.8574 (tt) cc_final: 0.8295 (pp) REVERT: A 374 MET cc_start: 0.6740 (tpt) cc_final: 0.5995 (tpt) REVERT: A 383 GLU cc_start: 0.7744 (pt0) cc_final: 0.7504 (pt0) REVERT: A 392 GLU cc_start: 0.7150 (tt0) cc_final: 0.6871 (mm-30) REVERT: A 417 ILE cc_start: 0.7832 (mm) cc_final: 0.7611 (mm) REVERT: A 439 VAL cc_start: 0.6634 (t) cc_final: 0.6243 (m) REVERT: A 443 ASN cc_start: 0.9299 (m-40) cc_final: 0.9075 (t0) REVERT: A 452 MET cc_start: 0.7528 (ttt) cc_final: 0.7199 (tpp) REVERT: A 655 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.6995 (ptm160) REVERT: A 660 LYS cc_start: 0.7518 (mttt) cc_final: 0.7258 (mmtm) REVERT: A 702 HIS cc_start: 0.7329 (m-70) cc_final: 0.6930 (m-70) REVERT: B 218 MET cc_start: 0.7298 (ttm) cc_final: 0.7032 (mtt) REVERT: B 243 GLU cc_start: 0.8711 (tp30) cc_final: 0.8492 (tt0) REVERT: B 248 GLU cc_start: 0.7216 (tp30) cc_final: 0.6960 (tp30) REVERT: B 267 ASN cc_start: 0.6832 (m-40) cc_final: 0.6604 (m-40) REVERT: B 292 LEU cc_start: 0.8587 (mt) cc_final: 0.8273 (mt) REVERT: B 316 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7032 (tp30) REVERT: B 345 PHE cc_start: 0.7333 (m-80) cc_final: 0.6845 (m-80) REVERT: B 360 GLU cc_start: 0.7579 (tt0) cc_final: 0.7370 (tm-30) REVERT: B 372 GLU cc_start: 0.6172 (tp30) cc_final: 0.5885 (tp30) REVERT: B 389 MET cc_start: 0.9184 (mmt) cc_final: 0.8666 (tmm) REVERT: B 416 GLN cc_start: 0.7558 (tp40) cc_final: 0.7284 (tp40) REVERT: B 428 TYR cc_start: 0.7588 (t80) cc_final: 0.7366 (t80) REVERT: B 430 TYR cc_start: 0.7824 (t80) cc_final: 0.7617 (t80) REVERT: B 446 TYR cc_start: 0.6981 (m-80) cc_final: 0.6772 (m-10) REVERT: B 452 ASN cc_start: 0.3719 (m-40) cc_final: 0.3458 (m-40) REVERT: X 1 MET cc_start: 0.4101 (ttm) cc_final: 0.3416 (ttt) REVERT: X 3 TRP cc_start: 0.6559 (t60) cc_final: 0.5842 (t60) REVERT: X 5 LEU cc_start: 0.6487 (OUTLIER) cc_final: 0.6242 (tt) REVERT: X 46 ASP cc_start: 0.6712 (p0) cc_final: 0.6489 (p0) outliers start: 5 outliers final: 2 residues processed: 366 average time/residue: 0.2151 time to fit residues: 101.8526 Evaluate side-chains 279 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 276 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain X residue 5 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 0.0570 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 35 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 overall best weight: 4.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN A 251 ASN A 257 HIS A 382 ASN A 401 ASN A 701 GLN B 171 HIS B 539 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5090 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7919 Z= 0.212 Angle : 0.571 10.522 10794 Z= 0.301 Chirality : 0.039 0.198 1301 Planarity : 0.004 0.049 1427 Dihedral : 4.322 48.223 1248 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.20 % Favored : 96.72 % Rotamer: Outliers : 6.42 % Allowed : 15.37 % Favored : 78.21 % 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: 0.70 (0.24), residues: 1158 helix: 1.72 (0.17), residues: 788 sheet: -3.67 (0.83), residues: 35 loop : -2.21 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 413 HIS 0.009 0.001 HIS B 299 PHE 0.016 0.002 PHE A 190 TYR 0.022 0.002 TYR X 22 ARG 0.007 0.001 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 293 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 LYS cc_start: 0.7154 (tttt) cc_final: 0.6795 (ttpt) REVERT: A 439 VAL cc_start: 0.6753 (t) cc_final: 0.5918 (t) REVERT: A 443 ASN cc_start: 0.9337 (m-40) cc_final: 0.9105 (t0) REVERT: A 660 LYS cc_start: 0.7572 (mttt) cc_final: 0.7311 (mmtm) REVERT: A 702 HIS cc_start: 0.7259 (m-70) cc_final: 0.6866 (m-70) REVERT: B 243 GLU cc_start: 0.8744 (tp30) cc_final: 0.8530 (tt0) REVERT: B 262 ASN cc_start: 0.8239 (t0) cc_final: 0.7992 (t0) REVERT: B 313 ARG cc_start: 0.8034 (ttt180) cc_final: 0.7813 (mtp180) REVERT: B 316 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6851 (tp30) REVERT: B 351 GLU cc_start: 0.8831 (tp30) cc_final: 0.8611 (tp30) REVERT: B 360 GLU cc_start: 0.7654 (tt0) cc_final: 0.7403 (tm-30) REVERT: B 389 MET cc_start: 0.9293 (mmt) cc_final: 0.8841 (tmm) REVERT: B 416 GLN cc_start: 0.8115 (tp40) cc_final: 0.7820 (tp40) REVERT: B 428 TYR cc_start: 0.7321 (t80) cc_final: 0.6986 (t80) REVERT: X 5 LEU cc_start: 0.6271 (OUTLIER) cc_final: 0.5862 (tt) outliers start: 38 outliers final: 23 residues processed: 309 average time/residue: 0.1818 time to fit residues: 76.0447 Evaluate side-chains 273 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 249 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 45 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 50.0000 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 105 optimal weight: 20.0000 chunk 114 optimal weight: 20.0000 chunk 93 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 35 optimal weight: 50.0000 chunk 84 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 171 HIS B 250 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5096 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7919 Z= 0.235 Angle : 0.586 10.734 10794 Z= 0.303 Chirality : 0.039 0.249 1301 Planarity : 0.004 0.035 1427 Dihedral : 4.288 40.129 1248 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.23 % Favored : 95.68 % Rotamer: Outliers : 8.11 % Allowed : 19.59 % Favored : 72.30 % 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: 1.19 (0.25), residues: 1158 helix: 2.02 (0.18), residues: 804 sheet: -3.57 (0.86), residues: 34 loop : -2.03 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 348 HIS 0.006 0.001 HIS B 299 PHE 0.031 0.002 PHE A 190 TYR 0.017 0.002 TYR A 349 ARG 0.016 0.001 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 256 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.8246 (t80) cc_final: 0.7857 (t80) REVERT: A 344 LYS cc_start: 0.7275 (tttt) cc_final: 0.6927 (ttpt) REVERT: A 439 VAL cc_start: 0.6706 (t) cc_final: 0.6008 (t) REVERT: A 443 ASN cc_start: 0.9319 (m-40) cc_final: 0.9075 (t0) REVERT: A 601 TYR cc_start: 0.6704 (t80) cc_final: 0.6030 (t80) REVERT: A 660 LYS cc_start: 0.7493 (mttt) cc_final: 0.7268 (mmtm) REVERT: A 702 HIS cc_start: 0.7104 (m-70) cc_final: 0.6688 (m-70) REVERT: B 345 PHE cc_start: 0.7588 (m-80) cc_final: 0.7100 (m-80) REVERT: B 351 GLU cc_start: 0.8923 (tp30) cc_final: 0.8608 (tp30) REVERT: B 360 GLU cc_start: 0.7516 (tt0) cc_final: 0.7272 (tm-30) REVERT: B 389 MET cc_start: 0.9288 (mmt) cc_final: 0.8839 (tmm) outliers start: 48 outliers final: 39 residues processed: 282 average time/residue: 0.1827 time to fit residues: 70.7015 Evaluate side-chains 280 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 241 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 401 ASN Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 275 LEU Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 25 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 54 optimal weight: 30.0000 chunk 11 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 112 optimal weight: 0.0770 chunk 55 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 30 optimal weight: 7.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN B 452 ASN B 539 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5077 moved from start: 0.4936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7919 Z= 0.217 Angle : 0.572 9.965 10794 Z= 0.294 Chirality : 0.038 0.182 1301 Planarity : 0.003 0.040 1427 Dihedral : 4.286 37.689 1248 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.37 % Favored : 96.55 % Rotamer: Outliers : 9.12 % Allowed : 23.65 % Favored : 67.23 % 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: 1.30 (0.25), residues: 1158 helix: 2.07 (0.18), residues: 805 sheet: -3.40 (0.86), residues: 34 loop : -1.91 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 348 HIS 0.004 0.001 HIS B 299 PHE 0.022 0.002 PHE A 447 TYR 0.013 0.002 TYR A 249 ARG 0.004 0.000 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 248 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.8226 (t80) cc_final: 0.7838 (t80) REVERT: A 344 LYS cc_start: 0.7330 (tttt) cc_final: 0.6976 (ttpt) REVERT: A 443 ASN cc_start: 0.9320 (m-40) cc_final: 0.9074 (t0) REVERT: A 601 TYR cc_start: 0.6472 (t80) cc_final: 0.5837 (t80) REVERT: B 285 MET cc_start: 0.8453 (mtm) cc_final: 0.8172 (mtm) REVERT: B 345 PHE cc_start: 0.7633 (m-80) cc_final: 0.7179 (m-80) REVERT: B 351 GLU cc_start: 0.8926 (tp30) cc_final: 0.8592 (tp30) REVERT: B 360 GLU cc_start: 0.7479 (tt0) cc_final: 0.7241 (tm-30) REVERT: B 389 MET cc_start: 0.9136 (mmt) cc_final: 0.8824 (tmm) outliers start: 54 outliers final: 38 residues processed: 279 average time/residue: 0.1749 time to fit residues: 66.4168 Evaluate side-chains 284 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 246 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 258 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 25 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 50.0000 chunk 63 optimal weight: 30.0000 chunk 1 optimal weight: 1.9990 chunk 83 optimal weight: 50.0000 chunk 46 optimal weight: 0.0670 chunk 95 optimal weight: 0.0010 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 overall best weight: 3.2130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN X 14 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5058 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7919 Z= 0.171 Angle : 0.559 9.584 10794 Z= 0.284 Chirality : 0.038 0.233 1301 Planarity : 0.003 0.036 1427 Dihedral : 4.121 39.313 1248 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.02 % Favored : 96.89 % Rotamer: Outliers : 7.09 % Allowed : 27.53 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 1158 helix: 2.20 (0.18), residues: 807 sheet: -3.38 (0.83), residues: 34 loop : -1.84 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 214 HIS 0.004 0.001 HIS B 299 PHE 0.015 0.002 PHE B 412 TYR 0.033 0.002 TYR A 249 ARG 0.006 0.001 ARG B 343 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 255 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 224 PHE cc_start: 0.8216 (t80) cc_final: 0.7864 (t80) REVERT: A 344 LYS cc_start: 0.7372 (tttt) cc_final: 0.7017 (ttpt) REVERT: A 443 ASN cc_start: 0.9321 (m-40) cc_final: 0.9112 (t0) REVERT: A 466 PRO cc_start: 0.8470 (Cg_endo) cc_final: 0.8243 (Cg_exo) REVERT: A 470 LYS cc_start: 0.9014 (tptm) cc_final: 0.8782 (mmtm) REVERT: A 601 TYR cc_start: 0.6304 (t80) cc_final: 0.5598 (t80) REVERT: B 285 MET cc_start: 0.8400 (mtm) cc_final: 0.8163 (mtm) REVERT: B 345 PHE cc_start: 0.7600 (m-80) cc_final: 0.7119 (m-80) REVERT: B 351 GLU cc_start: 0.8927 (tp30) cc_final: 0.8606 (tp30) REVERT: B 389 MET cc_start: 0.9130 (mmt) cc_final: 0.8776 (tmm) REVERT: B 450 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.7093 (pp30) outliers start: 42 outliers final: 32 residues processed: 271 average time/residue: 0.1864 time to fit residues: 68.9500 Evaluate side-chains 275 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 242 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 14 ASN Chi-restraints excluded: chain X residue 25 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.7980 chunk 100 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 112 optimal weight: 0.0770 chunk 93 optimal weight: 50.0000 chunk 51 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 overall best weight: 2.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5062 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7919 Z= 0.174 Angle : 0.583 9.304 10794 Z= 0.295 Chirality : 0.038 0.173 1301 Planarity : 0.003 0.033 1427 Dihedral : 4.078 39.402 1248 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.85 % Favored : 97.06 % Rotamer: Outliers : 7.77 % Allowed : 27.87 % Favored : 64.36 % 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: 1.58 (0.26), residues: 1158 helix: 2.24 (0.18), residues: 807 sheet: -3.31 (0.82), residues: 34 loop : -1.71 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 214 HIS 0.004 0.001 HIS B 299 PHE 0.023 0.002 PHE B 412 TYR 0.028 0.002 TYR A 249 ARG 0.006 0.000 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 243 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.8236 (t80) cc_final: 0.7858 (t80) REVERT: A 344 LYS cc_start: 0.7420 (tttt) cc_final: 0.7102 (pttt) REVERT: A 443 ASN cc_start: 0.9334 (m-40) cc_final: 0.9126 (t0) REVERT: A 601 TYR cc_start: 0.6188 (t80) cc_final: 0.5401 (t80) REVERT: B 345 PHE cc_start: 0.7551 (m-80) cc_final: 0.7002 (m-80) REVERT: B 351 GLU cc_start: 0.8936 (tp30) cc_final: 0.8617 (tp30) REVERT: B 389 MET cc_start: 0.9036 (mmt) cc_final: 0.8690 (tmm) REVERT: B 450 GLN cc_start: 0.7492 (OUTLIER) cc_final: 0.7162 (pp30) outliers start: 46 outliers final: 32 residues processed: 262 average time/residue: 0.1861 time to fit residues: 65.9764 Evaluate side-chains 260 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 227 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 539 HIS Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 45 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 81 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 44 optimal weight: 40.0000 chunk 66 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5081 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7919 Z= 0.263 Angle : 0.654 10.352 10794 Z= 0.333 Chirality : 0.040 0.196 1301 Planarity : 0.003 0.031 1427 Dihedral : 4.535 39.512 1248 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 8.78 % Allowed : 26.01 % Favored : 65.20 % 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: 1.30 (0.25), residues: 1158 helix: 1.97 (0.18), residues: 806 sheet: -3.31 (0.71), residues: 44 loop : -1.54 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 214 HIS 0.005 0.001 HIS A 257 PHE 0.015 0.002 PHE B 412 TYR 0.022 0.002 TYR A 249 ARG 0.007 0.001 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 238 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.8104 (t80) cc_final: 0.7767 (t80) REVERT: A 344 LYS cc_start: 0.7324 (tttt) cc_final: 0.7005 (pttt) REVERT: A 601 TYR cc_start: 0.5925 (t80) cc_final: 0.5178 (t80) REVERT: B 187 HIS cc_start: 0.8827 (m-70) cc_final: 0.8484 (p90) REVERT: B 345 PHE cc_start: 0.7546 (m-80) cc_final: 0.7097 (m-80) REVERT: B 351 GLU cc_start: 0.8966 (tp30) cc_final: 0.8679 (tp30) REVERT: B 389 MET cc_start: 0.9138 (mmt) cc_final: 0.8809 (tmm) REVERT: B 447 MET cc_start: 0.7042 (mtp) cc_final: 0.6830 (mtp) REVERT: B 450 GLN cc_start: 0.7424 (OUTLIER) cc_final: 0.7121 (pp30) REVERT: B 477 TYR cc_start: 0.6241 (OUTLIER) cc_final: 0.6007 (m-10) outliers start: 52 outliers final: 41 residues processed: 264 average time/residue: 0.1861 time to fit residues: 66.6655 Evaluate side-chains 269 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 42 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 40.0000 chunk 21 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 107 optimal weight: 50.0000 chunk 97 optimal weight: 0.7980 chunk 104 optimal weight: 20.0000 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5069 moved from start: 0.6242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7919 Z= 0.258 Angle : 0.649 10.148 10794 Z= 0.338 Chirality : 0.041 0.237 1301 Planarity : 0.003 0.036 1427 Dihedral : 4.614 39.124 1248 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.63 % Favored : 96.29 % Rotamer: Outliers : 8.78 % Allowed : 26.18 % Favored : 65.03 % 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: 1.15 (0.26), residues: 1158 helix: 1.81 (0.18), residues: 816 sheet: -3.07 (0.74), residues: 44 loop : -1.62 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 214 HIS 0.004 0.001 HIS B 299 PHE 0.017 0.002 PHE B 412 TYR 0.031 0.002 TYR B 310 ARG 0.008 0.001 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 235 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.8020 (t80) cc_final: 0.7678 (t80) REVERT: A 344 LYS cc_start: 0.7370 (tttt) cc_final: 0.7038 (tttt) REVERT: A 470 LYS cc_start: 0.9067 (tptm) cc_final: 0.8854 (mmtt) REVERT: A 601 TYR cc_start: 0.5811 (t80) cc_final: 0.5174 (t80) REVERT: B 187 HIS cc_start: 0.8821 (m-70) cc_final: 0.8482 (p90) REVERT: B 345 PHE cc_start: 0.7557 (m-80) cc_final: 0.7166 (m-80) REVERT: B 351 GLU cc_start: 0.8979 (tp30) cc_final: 0.8689 (tp30) REVERT: B 389 MET cc_start: 0.9135 (mmt) cc_final: 0.8805 (tmm) REVERT: B 450 GLN cc_start: 0.7439 (OUTLIER) cc_final: 0.7126 (pp30) REVERT: B 477 TYR cc_start: 0.6216 (OUTLIER) cc_final: 0.5998 (m-10) outliers start: 52 outliers final: 43 residues processed: 261 average time/residue: 0.1912 time to fit residues: 68.9876 Evaluate side-chains 273 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain B residue 450 GLN Chi-restraints excluded: chain B residue 477 TYR Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 42 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 50.0000 chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 50.0000 chunk 81 optimal weight: 20.0000 chunk 31 optimal weight: 50.0000 chunk 94 optimal weight: 30.0000 chunk 98 optimal weight: 30.0000 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 110 optimal weight: 50.0000 chunk 67 optimal weight: 5.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 250 ASN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5060 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7919 Z= 0.307 Angle : 0.715 10.021 10794 Z= 0.372 Chirality : 0.043 0.267 1301 Planarity : 0.004 0.041 1427 Dihedral : 4.962 39.522 1248 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.44 % Favored : 94.47 % Rotamer: Outliers : 8.28 % Allowed : 28.38 % Favored : 63.34 % 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: 0.81 (0.26), residues: 1158 helix: 1.52 (0.18), residues: 813 sheet: -2.93 (0.75), residues: 45 loop : -1.60 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 214 HIS 0.005 0.001 HIS A 255 PHE 0.017 0.002 PHE B 412 TYR 0.040 0.003 TYR A 249 ARG 0.010 0.001 ARG X 41 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 232 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.7913 (t80) cc_final: 0.7585 (t80) REVERT: A 253 MET cc_start: 0.8690 (mtt) cc_final: 0.8449 (mtm) REVERT: A 344 LYS cc_start: 0.7316 (tttt) cc_final: 0.6968 (tttt) REVERT: A 386 GLU cc_start: 0.8845 (tp30) cc_final: 0.8475 (tp30) REVERT: A 420 MET cc_start: 0.8769 (mpp) cc_final: 0.8475 (pmm) REVERT: A 428 TYR cc_start: 0.7892 (t80) cc_final: 0.7679 (t80) REVERT: A 601 TYR cc_start: 0.5605 (t80) cc_final: 0.4958 (t80) REVERT: B 187 HIS cc_start: 0.8830 (m-70) cc_final: 0.8503 (p90) REVERT: B 345 PHE cc_start: 0.7623 (m-80) cc_final: 0.7214 (m-80) REVERT: B 351 GLU cc_start: 0.8982 (tp30) cc_final: 0.8692 (tp30) REVERT: B 389 MET cc_start: 0.9173 (mmt) cc_final: 0.8852 (tmm) REVERT: B 556 PHE cc_start: 0.6275 (m-80) cc_final: 0.5427 (m-80) outliers start: 49 outliers final: 45 residues processed: 258 average time/residue: 0.1742 time to fit residues: 61.3603 Evaluate side-chains 271 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 226 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 242 GLU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 106 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 73 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5051 moved from start: 0.6785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7919 Z= 0.264 Angle : 0.707 11.940 10794 Z= 0.364 Chirality : 0.042 0.275 1301 Planarity : 0.004 0.038 1427 Dihedral : 4.639 38.693 1245 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.97 % Favored : 95.94 % Rotamer: Outliers : 7.77 % Allowed : 29.90 % Favored : 62.33 % 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: 0.89 (0.26), residues: 1158 helix: 1.57 (0.18), residues: 810 sheet: -2.66 (0.78), residues: 45 loop : -1.56 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 214 HIS 0.004 0.001 HIS B 299 PHE 0.020 0.002 PHE B 412 TYR 0.040 0.003 TYR B 310 ARG 0.012 0.001 ARG X 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 233 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 PHE cc_start: 0.7897 (t80) cc_final: 0.7584 (t80) REVERT: A 344 LYS cc_start: 0.7320 (tttt) cc_final: 0.6985 (tttt) REVERT: A 420 MET cc_start: 0.8781 (mpp) cc_final: 0.8502 (pmm) REVERT: A 428 TYR cc_start: 0.7892 (t80) cc_final: 0.7683 (t80) REVERT: A 601 TYR cc_start: 0.5541 (t80) cc_final: 0.4884 (t80) REVERT: B 187 HIS cc_start: 0.8837 (m-70) cc_final: 0.8510 (p90) REVERT: B 345 PHE cc_start: 0.7624 (m-80) cc_final: 0.7214 (m-80) REVERT: B 351 GLU cc_start: 0.8972 (tp30) cc_final: 0.8682 (tp30) REVERT: B 389 MET cc_start: 0.9146 (mmt) cc_final: 0.8830 (tmm) REVERT: B 450 GLN cc_start: 0.7794 (pm20) cc_final: 0.7320 (tp40) outliers start: 46 outliers final: 43 residues processed: 256 average time/residue: 0.1814 time to fit residues: 63.5622 Evaluate side-chains 275 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 232 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 288 VAL Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 350 GLN Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 354 VAL Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 383 GLU Chi-restraints excluded: chain A residue 406 VAL Chi-restraints excluded: chain A residue 414 THR Chi-restraints excluded: chain A residue 416 SER Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 139 TRP Chi-restraints excluded: chain B residue 142 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain B residue 251 SER Chi-restraints excluded: chain B residue 284 PHE Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 288 ILE Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain B residue 426 LEU Chi-restraints excluded: chain B residue 449 ARG Chi-restraints excluded: chain X residue 5 LEU Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 25 VAL Chi-restraints excluded: chain X residue 42 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 40.0000 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 11 optimal weight: 50.0000 chunk 16 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 5 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 451 GLN ** B 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.153538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.133147 restraints weight = 20164.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.135943 restraints weight = 13502.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137907 restraints weight = 10010.041| |-----------------------------------------------------------------------------| r_work (final): 0.3766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.6914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7919 Z= 0.227 Angle : 0.710 11.206 10794 Z= 0.358 Chirality : 0.041 0.256 1301 Planarity : 0.003 0.030 1427 Dihedral : 4.456 37.562 1245 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer: Outliers : 7.43 % Allowed : 30.91 % Favored : 61.66 % 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 (0.26), residues: 1158 helix: 1.72 (0.19), residues: 809 sheet: -2.52 (0.79), residues: 45 loop : -1.49 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 214 HIS 0.004 0.001 HIS B 299 PHE 0.022 0.002 PHE B 412 TYR 0.052 0.002 TYR A 249 ARG 0.011 0.001 ARG X 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2844.46 seconds wall clock time: 51 minutes 18.70 seconds (3078.70 seconds total)