Starting phenix.real_space_refine on Fri Nov 15 01:16:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t46_41021/11_2024/8t46_41021.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t46_41021/11_2024/8t46_41021.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t46_41021/11_2024/8t46_41021.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t46_41021/11_2024/8t46_41021.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t46_41021/11_2024/8t46_41021.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t46_41021/11_2024/8t46_41021.cif" } resolution = 3.6 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= 0.021 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 33 5.16 5 C 4980 2.51 5 N 1394 2.21 5 O 1478 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7885 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 3661 Classifications: {'peptide': 562} Incomplete info: {'truncation_to_alanine': 204} Link IDs: {'PTRANS': 18, 'TRANS': 543} Chain breaks: 1 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 725 Unresolved non-hydrogen angles: 937 Unresolved non-hydrogen dihedrals: 586 Unresolved non-hydrogen chiralities: 76 Planarities with less than four sites: {'GLN:plan1': 24, 'ARG:plan': 11, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 16, 'HIS:plan': 7} Unresolved non-hydrogen planarities: 400 Chain: "B" Number of atoms: 4224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 551, 4224 Classifications: {'peptide': 551} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 20, 'TRANS': 530} Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 62 Time building chain proxies: 5.91, per 1000 atoms: 0.75 Number of scatterers: 7885 At special positions: 0 Unit cell: (73.832, 122.494, 139.274, 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 33 16.00 O 1478 8.00 N 1394 7.00 C 4980 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 - 3.00 Amino acid : True - 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: 1.99 Conformation dependent library (CDL) restraints added in 1.3 seconds 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2050 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 73.5% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.138A pdb=" N LEU A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 202 removed outlier: 4.139A pdb=" N LEU A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N MET A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 4.319A pdb=" N PHE A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 270 removed outlier: 3.668A pdb=" N ASN A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 281 through 324 removed outlier: 4.010A pdb=" N MET A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N THR A 289 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 340 removed outlier: 4.767A pdb=" N VAL A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) Proline residue: A 336 - end of helix Processing helix chain 'A' and resid 340 through 373 removed outlier: 3.959A pdb=" N LYS A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TYR A 349 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 382 through 421 removed outlier: 4.255A pdb=" N THR A 399 " --> pdb=" O GLN A 395 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 437 removed outlier: 3.750A pdb=" N LEU A 427 " --> pdb=" O LYS A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 462 Processing helix chain 'A' and resid 464 through 484 removed outlier: 3.577A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 627 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.716A pdb=" N ASP A 633 " --> pdb=" O GLN A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 641 removed outlier: 3.554A pdb=" N GLY A 640 " --> pdb=" O ASP A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 Processing helix chain 'A' and resid 674 through 687 Processing helix chain 'A' and resid 688 through 694 removed outlier: 3.891A pdb=" N TYR A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 694 " --> pdb=" O ARG A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.705A pdb=" N GLN A 708 " --> pdb=" O SER A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'B' and resid 132 through 146 Processing helix chain 'B' and resid 148 through 167 Processing helix chain 'B' and resid 167 through 181 removed outlier: 4.040A pdb=" N HIS B 171 " --> pdb=" O THR B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 234 Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.820A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 262 removed outlier: 4.811A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 289 removed outlier: 3.930A pdb=" N LEU B 266 " --> pdb=" O ASN B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 298 Processing helix chain 'B' and resid 299 through 346 removed outlier: 3.616A pdb=" N GLU B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLN B 340 " --> pdb=" O VAL B 336 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR B 341 " --> pdb=" O GLY B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 402 removed outlier: 4.159A pdb=" N ARG B 354 " --> pdb=" O HIS B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 437 removed outlier: 4.491A pdb=" N GLY B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TYR B 422 " --> pdb=" O SER B 418 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N TYR B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU B 434 " --> pdb=" O TYR B 430 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 435 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 Processing helix chain 'B' and resid 509 through 515 removed outlier: 3.661A pdb=" N ALA B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU B 515 " --> pdb=" O THR B 511 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 545 removed outlier: 3.950A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER B 544 " --> pdb=" O CYS B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 573 through 583 removed outlier: 4.091A pdb=" N MET B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA B 578 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ALA B 579 " --> pdb=" O LYS B 575 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 580 " --> pdb=" O VAL B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 592 removed outlier: 3.520A pdb=" N GLN B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU B 591 " --> pdb=" O ASP B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 623 removed outlier: 4.238A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 removed outlier: 4.082A pdb=" N ALA B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 647 removed outlier: 3.668A pdb=" N GLU B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 Processing helix chain 'B' and resid 662 through 668 removed outlier: 4.008A pdb=" N THR B 665 " --> pdb=" O ARG B 662 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN B 667 " --> pdb=" O GLN B 664 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 519 through 524 removed outlier: 5.745A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 508 " --> pdb=" O LEU A 524 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N PHE A 505 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 563 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ASP A 507 " --> pdb=" O GLN A 561 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N GLN A 561 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 581 through 584 removed outlier: 3.812A pdb=" N VAL A 584 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 667 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU A 664 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE A 699 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LEU A 666 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N THR A 534 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLU A 716 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 489 through 492 removed outlier: 4.910A pdb=" N LEU B 489 " --> pdb=" O ASP B 472 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE B 470 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU B 528 " --> pdb=" O PHE B 470 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ASP B 472 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLN B 526 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 546 through 548 removed outlier: 6.963A pdb=" N VAL B 547 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ASP B 631 " --> pdb=" O VAL B 547 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR B 499 " --> pdb=" O VAL B 658 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N ALA B 660 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU B 501 " --> pdb=" O ALA B 660 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) 589 hydrogen bonds defined for protein. 1728 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: 2.48 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2690 1.34 - 1.46: 1645 1.46 - 1.58: 3610 1.58 - 1.70: 0 1.70 - 1.81: 56 Bond restraints: 8001 Sorted by residual: bond pdb=" N GLU A 201 " pdb=" CA GLU A 201 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.70e+00 bond pdb=" N ASP B 573 " pdb=" CA ASP B 573 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.28e-02 6.10e+03 6.07e+00 bond pdb=" N LEU B 385 " pdb=" CA LEU B 385 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.20e-02 6.94e+03 5.85e+00 bond pdb=" N ASN B 222 " pdb=" CA ASN B 222 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.19e-02 7.06e+03 5.73e+00 bond pdb=" N MET A 202 " pdb=" CA MET A 202 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.64e+00 ... (remaining 7996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 10760 2.33 - 4.65: 99 4.65 - 6.98: 18 6.98 - 9.31: 6 9.31 - 11.63: 1 Bond angle restraints: 10884 Sorted by residual: angle pdb=" C LYS B 575 " pdb=" N VAL B 576 " pdb=" CA VAL B 576 " ideal model delta sigma weight residual 122.63 117.56 5.07 1.19e+00 7.06e-01 1.81e+01 angle pdb=" CB MET B 218 " pdb=" CG MET B 218 " pdb=" SD MET B 218 " ideal model delta sigma weight residual 112.70 124.33 -11.63 3.00e+00 1.11e-01 1.50e+01 angle pdb=" N THR A 223 " pdb=" CA THR A 223 " pdb=" C THR A 223 " ideal model delta sigma weight residual 113.01 108.69 4.32 1.20e+00 6.94e-01 1.30e+01 angle pdb=" CA MET B 218 " pdb=" CB MET B 218 " pdb=" CG MET B 218 " ideal model delta sigma weight residual 114.10 120.50 -6.40 2.00e+00 2.50e-01 1.03e+01 angle pdb=" C MET A 202 " pdb=" N ALA A 203 " pdb=" CA ALA A 203 " ideal model delta sigma weight residual 122.06 116.22 5.84 1.86e+00 2.89e-01 9.86e+00 ... (remaining 10879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 4134 17.50 - 35.00: 457 35.00 - 52.50: 141 52.50 - 70.01: 18 70.01 - 87.51: 10 Dihedral angle restraints: 4760 sinusoidal: 1574 harmonic: 3186 Sorted by residual: dihedral pdb=" CA ARG A 287 " pdb=" C ARG A 287 " pdb=" N VAL A 288 " pdb=" CA VAL A 288 " ideal model delta harmonic sigma weight residual -180.00 -159.76 -20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ASP B 472 " pdb=" CB ASP B 472 " pdb=" CG ASP B 472 " pdb=" OD1 ASP B 472 " ideal model delta sinusoidal sigma weight residual -30.00 -88.39 58.39 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASN A 283 " pdb=" C ASN A 283 " pdb=" N ILE A 284 " pdb=" CA ILE A 284 " ideal model delta harmonic sigma weight residual 180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 4757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1033 0.048 - 0.096: 218 0.096 - 0.144: 49 0.144 - 0.192: 3 0.192 - 0.240: 1 Chirality restraints: 1304 Sorted by residual: chirality pdb=" CG LEU A 327 " pdb=" CB LEU A 327 " pdb=" CD1 LEU A 327 " pdb=" CD2 LEU A 327 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CA MET A 374 " pdb=" N MET A 374 " pdb=" C MET A 374 " pdb=" CB MET A 374 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.03e-01 chirality pdb=" CA LEU B 385 " pdb=" N LEU B 385 " pdb=" C LEU B 385 " pdb=" CB LEU B 385 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.94e-01 ... (remaining 1301 not shown) Planarity restraints: 1421 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 306 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.91e+00 pdb=" C PHE A 306 " 0.052 2.00e-02 2.50e+03 pdb=" O PHE A 306 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU A 307 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 301 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.40e+00 pdb=" C GLU A 301 " -0.050 2.00e-02 2.50e+03 pdb=" O GLU A 301 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 302 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 305 " 0.014 2.00e-02 2.50e+03 2.85e-02 8.10e+00 pdb=" C LEU A 305 " -0.049 2.00e-02 2.50e+03 pdb=" O LEU A 305 " 0.019 2.00e-02 2.50e+03 pdb=" N PHE A 306 " 0.016 2.00e-02 2.50e+03 ... (remaining 1418 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2131 2.80 - 3.33: 7880 3.33 - 3.85: 12995 3.85 - 4.38: 13091 4.38 - 4.90: 23591 Nonbonded interactions: 59688 Sorted by model distance: nonbonded pdb=" O GLN A 278 " pdb=" OG1 THR A 281 " model vdw 2.278 3.040 nonbonded pdb=" O PHE B 158 " pdb=" OG SER B 206 " model vdw 2.282 3.040 nonbonded pdb=" OG SER A 440 " pdb=" OD1 ASN A 443 " model vdw 2.300 3.040 nonbonded pdb=" OE1 GLU B 307 " pdb=" OH TYR B 376 " model vdw 2.314 3.040 nonbonded pdb=" O PRO B 461 " pdb=" OH TYR B 541 " model vdw 2.324 3.040 ... (remaining 59683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.170 Find NCS groups from input model: 0.120 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8001 Z= 0.217 Angle : 0.633 11.634 10884 Z= 0.354 Chirality : 0.041 0.240 1304 Planarity : 0.006 0.047 1421 Dihedral : 16.789 87.506 2710 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.08 % Favored : 97.83 % Rotamer: Outliers : 0.28 % Allowed : 27.97 % Favored : 71.75 % 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: 1.31 (0.25), residues: 1107 helix: 1.28 (0.19), residues: 757 sheet: 0.94 (0.69), residues: 64 loop : -0.08 (0.36), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 214 HIS 0.005 0.001 HIS B 299 PHE 0.009 0.001 PHE B 491 TYR 0.021 0.001 TYR A 481 ARG 0.002 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 242 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7847 (tt0) REVERT: A 451 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8069 (tm-30) REVERT: A 465 TYR cc_start: 0.6256 (t80) cc_final: 0.6047 (t80) REVERT: B 424 GLN cc_start: 0.9013 (tt0) cc_final: 0.8591 (tp40) outliers start: 2 outliers final: 0 residues processed: 110 average time/residue: 0.1819 time to fit residues: 28.1967 Evaluate side-chains 85 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 52 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN A 302 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8001 Z= 0.241 Angle : 0.519 6.614 10884 Z= 0.271 Chirality : 0.038 0.133 1304 Planarity : 0.003 0.044 1421 Dihedral : 3.369 15.426 1183 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.34 % Allowed : 25.87 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.26), residues: 1107 helix: 1.91 (0.19), residues: 767 sheet: 0.81 (0.71), residues: 63 loop : 0.49 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 367 HIS 0.007 0.001 HIS B 299 PHE 0.010 0.001 PHE B 470 TYR 0.012 0.001 TYR B 366 ARG 0.002 0.000 ARG B 368 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7331 (t-100) cc_final: 0.6802 (t-100) REVERT: A 242 GLU cc_start: 0.8512 (tm-30) cc_final: 0.7970 (tt0) REVERT: A 285 MET cc_start: 0.7570 (mpp) cc_final: 0.7175 (mpp) REVERT: A 335 LEU cc_start: 0.7794 (tt) cc_final: 0.7242 (tp) REVERT: A 451 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8120 (tm-30) REVERT: A 465 TYR cc_start: 0.6306 (t80) cc_final: 0.5805 (t80) REVERT: A 469 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.6978 (mm110) REVERT: B 179 ILE cc_start: 0.8169 (mm) cc_final: 0.7913 (mm) REVERT: B 399 MET cc_start: 0.8360 (tpp) cc_final: 0.7962 (ttm) REVERT: B 401 ASP cc_start: 0.7772 (m-30) cc_final: 0.7427 (t0) REVERT: B 424 GLN cc_start: 0.9039 (tt0) cc_final: 0.8617 (tp40) outliers start: 31 outliers final: 17 residues processed: 111 average time/residue: 0.1532 time to fit residues: 25.1281 Evaluate side-chains 96 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 680 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 83 optimal weight: 0.0980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 100 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 302 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8001 Z= 0.156 Angle : 0.465 6.693 10884 Z= 0.241 Chirality : 0.036 0.130 1304 Planarity : 0.003 0.044 1421 Dihedral : 3.159 15.023 1183 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.48 % Allowed : 26.71 % Favored : 68.81 % 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: 2.62 (0.26), residues: 1107 helix: 2.29 (0.19), residues: 760 sheet: 0.54 (0.80), residues: 50 loop : 0.59 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 367 HIS 0.007 0.001 HIS B 299 PHE 0.011 0.001 PHE A 447 TYR 0.014 0.001 TYR A 481 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7243 (t-100) cc_final: 0.6637 (t-100) REVERT: A 242 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8042 (tt0) REVERT: A 285 MET cc_start: 0.7637 (mpp) cc_final: 0.7057 (mpp) REVERT: A 335 LEU cc_start: 0.7799 (tt) cc_final: 0.7240 (tp) REVERT: A 451 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8124 (tm-30) REVERT: A 465 TYR cc_start: 0.6238 (t80) cc_final: 0.5783 (t80) REVERT: A 469 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.6986 (mm110) REVERT: B 235 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7623 (ttm-80) REVERT: B 399 MET cc_start: 0.8330 (tpp) cc_final: 0.7981 (ttm) REVERT: B 401 ASP cc_start: 0.7727 (m-30) cc_final: 0.7451 (t0) REVERT: B 424 GLN cc_start: 0.9037 (tt0) cc_final: 0.8623 (tp40) REVERT: B 453 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8697 (mm) outliers start: 32 outliers final: 20 residues processed: 114 average time/residue: 0.1765 time to fit residues: 28.9517 Evaluate side-chains 100 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 680 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 11 optimal weight: 0.2980 chunk 48 optimal weight: 9.9990 chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 96 optimal weight: 0.0060 chunk 28 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 60 optimal weight: 0.7980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8001 Z= 0.135 Angle : 0.457 7.579 10884 Z= 0.235 Chirality : 0.036 0.131 1304 Planarity : 0.003 0.042 1421 Dihedral : 3.040 14.708 1183 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 4.62 % Allowed : 26.57 % Favored : 68.81 % 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: 2.82 (0.26), residues: 1107 helix: 2.45 (0.19), residues: 765 sheet: 0.60 (0.82), residues: 50 loop : 0.61 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 367 HIS 0.007 0.001 HIS B 299 PHE 0.009 0.001 PHE A 447 TYR 0.012 0.001 TYR B 366 ARG 0.007 0.000 ARG B 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7221 (t-100) cc_final: 0.6583 (t-100) REVERT: A 222 ASP cc_start: 0.7363 (p0) cc_final: 0.7041 (t0) REVERT: A 242 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8009 (tt0) REVERT: A 285 MET cc_start: 0.7605 (mpp) cc_final: 0.7107 (mpp) REVERT: A 335 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7256 (tp) REVERT: A 451 GLN cc_start: 0.8463 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 465 TYR cc_start: 0.6266 (t80) cc_final: 0.5790 (t80) REVERT: A 469 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7001 (mm110) REVERT: B 235 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7642 (ttm-80) REVERT: B 399 MET cc_start: 0.8319 (tpp) cc_final: 0.7965 (ttm) REVERT: B 401 ASP cc_start: 0.7701 (m-30) cc_final: 0.7426 (t0) REVERT: B 424 GLN cc_start: 0.9027 (tt0) cc_final: 0.8629 (tp40) REVERT: B 453 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8700 (mm) outliers start: 33 outliers final: 20 residues processed: 109 average time/residue: 0.1549 time to fit residues: 24.7041 Evaluate side-chains 103 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 656 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 30.0000 chunk 96 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 8001 Z= 0.334 Angle : 0.577 8.822 10884 Z= 0.296 Chirality : 0.040 0.137 1304 Planarity : 0.003 0.043 1421 Dihedral : 3.399 15.596 1183 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 6.57 % Allowed : 25.31 % Favored : 68.11 % 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: 2.42 (0.26), residues: 1107 helix: 2.10 (0.19), residues: 765 sheet: 0.58 (0.78), residues: 57 loop : 0.57 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 367 HIS 0.006 0.001 HIS B 299 PHE 0.018 0.002 PHE A 447 TYR 0.017 0.002 TYR B 282 ARG 0.002 0.000 ARG B 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 81 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7591 (t-100) cc_final: 0.7072 (t-100) REVERT: A 222 ASP cc_start: 0.7336 (p0) cc_final: 0.7109 (t0) REVERT: A 242 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8087 (tt0) REVERT: A 285 MET cc_start: 0.7716 (mpp) cc_final: 0.7169 (mpp) REVERT: A 335 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7395 (tp) REVERT: A 404 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7200 (tp30) REVERT: A 451 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8213 (tm-30) REVERT: A 465 TYR cc_start: 0.6493 (t80) cc_final: 0.6038 (t80) REVERT: A 469 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.6925 (mm110) REVERT: B 235 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7803 (ttm-80) REVERT: B 401 ASP cc_start: 0.7799 (m-30) cc_final: 0.7526 (t0) REVERT: B 586 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7300 (p0) outliers start: 47 outliers final: 31 residues processed: 123 average time/residue: 0.1625 time to fit residues: 29.4213 Evaluate side-chains 115 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 248 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 61 optimal weight: 0.1980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7812 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8001 Z= 0.197 Angle : 0.504 7.725 10884 Z= 0.262 Chirality : 0.037 0.132 1304 Planarity : 0.003 0.045 1421 Dihedral : 3.265 15.369 1183 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.31 % Allowed : 26.43 % Favored : 68.25 % 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: 2.63 (0.26), residues: 1107 helix: 2.29 (0.19), residues: 766 sheet: 0.59 (0.79), residues: 57 loop : 0.56 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 367 HIS 0.007 0.001 HIS B 299 PHE 0.016 0.001 PHE A 275 TYR 0.012 0.001 TYR A 481 ARG 0.003 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 85 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7566 (t-100) cc_final: 0.7036 (t-100) REVERT: A 242 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8076 (tt0) REVERT: A 285 MET cc_start: 0.7664 (mpp) cc_final: 0.7137 (mpp) REVERT: A 287 ARG cc_start: 0.7862 (mmm160) cc_final: 0.7442 (mmm160) REVERT: A 335 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7406 (tp) REVERT: A 404 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7076 (tp30) REVERT: A 451 GLN cc_start: 0.8526 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 465 TYR cc_start: 0.6417 (t80) cc_final: 0.6023 (t80) REVERT: A 469 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.6966 (mm110) REVERT: B 235 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7795 (ttm-80) REVERT: B 401 ASP cc_start: 0.7777 (m-30) cc_final: 0.7518 (t0) REVERT: B 424 GLN cc_start: 0.9059 (tt0) cc_final: 0.8642 (tp40) REVERT: B 586 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.7353 (p0) outliers start: 38 outliers final: 27 residues processed: 118 average time/residue: 0.1561 time to fit residues: 27.1344 Evaluate side-chains 112 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 656 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 3.9990 chunk 60 optimal weight: 0.1980 chunk 90 optimal weight: 0.0670 chunk 59 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 30.0000 overall best weight: 0.5318 ------------------------------------------------------------------------------- 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: 0.7768 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8001 Z= 0.145 Angle : 0.466 7.295 10884 Z= 0.241 Chirality : 0.036 0.130 1304 Planarity : 0.003 0.046 1421 Dihedral : 3.104 14.888 1183 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.90 % Allowed : 26.71 % Favored : 68.39 % 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: 2.81 (0.26), residues: 1107 helix: 2.49 (0.19), residues: 765 sheet: 0.26 (0.81), residues: 50 loop : 0.53 (0.38), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 367 HIS 0.007 0.001 HIS B 299 PHE 0.009 0.001 PHE A 447 TYR 0.012 0.001 TYR A 481 ARG 0.002 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 84 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7520 (t-100) cc_final: 0.7022 (t-100) REVERT: A 242 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8027 (tt0) REVERT: A 285 MET cc_start: 0.7643 (mpp) cc_final: 0.7139 (mpp) REVERT: A 287 ARG cc_start: 0.7953 (mmm160) cc_final: 0.7437 (mmm160) REVERT: A 335 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7390 (tp) REVERT: A 404 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7009 (tp30) REVERT: A 451 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8143 (tm-30) REVERT: A 465 TYR cc_start: 0.6374 (t80) cc_final: 0.5940 (t80) REVERT: A 469 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.6983 (mm110) REVERT: B 235 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7785 (ttm-80) REVERT: B 401 ASP cc_start: 0.7717 (m-30) cc_final: 0.7469 (t0) REVERT: B 424 GLN cc_start: 0.9077 (tt0) cc_final: 0.8681 (tp40) outliers start: 35 outliers final: 28 residues processed: 114 average time/residue: 0.1609 time to fit residues: 26.9511 Evaluate side-chains 112 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 235 ARG Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 656 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 chunk 102 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7793 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8001 Z= 0.174 Angle : 0.486 8.276 10884 Z= 0.249 Chirality : 0.037 0.130 1304 Planarity : 0.003 0.045 1421 Dihedral : 3.115 15.150 1183 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 5.03 % Allowed : 26.99 % Favored : 67.97 % 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: 2.81 (0.26), residues: 1107 helix: 2.46 (0.19), residues: 765 sheet: 0.51 (0.78), residues: 57 loop : 0.57 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 367 HIS 0.007 0.001 HIS B 299 PHE 0.012 0.001 PHE A 447 TYR 0.015 0.001 TYR B 366 ARG 0.001 0.000 ARG A 287 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7591 (t-100) cc_final: 0.7128 (t-100) REVERT: A 242 GLU cc_start: 0.8598 (tm-30) cc_final: 0.8072 (tt0) REVERT: A 285 MET cc_start: 0.7663 (mpp) cc_final: 0.7149 (mpp) REVERT: A 287 ARG cc_start: 0.7917 (mmm160) cc_final: 0.7374 (mmm160) REVERT: A 335 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7416 (tp) REVERT: A 404 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7020 (tp30) REVERT: A 451 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 465 TYR cc_start: 0.6453 (t80) cc_final: 0.6030 (t80) REVERT: A 469 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.6952 (mm110) REVERT: B 401 ASP cc_start: 0.7702 (m-30) cc_final: 0.7473 (t0) REVERT: B 424 GLN cc_start: 0.9087 (tt0) cc_final: 0.8693 (tp40) outliers start: 36 outliers final: 30 residues processed: 112 average time/residue: 0.1515 time to fit residues: 25.3780 Evaluate side-chains 113 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 656 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 0.8980 chunk 60 optimal weight: 0.0970 chunk 43 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 99 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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: 0.7776 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8001 Z= 0.159 Angle : 0.485 8.025 10884 Z= 0.247 Chirality : 0.036 0.132 1304 Planarity : 0.003 0.046 1421 Dihedral : 3.078 14.961 1183 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 5.03 % Allowed : 27.27 % Favored : 67.69 % 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: 2.85 (0.26), residues: 1107 helix: 2.50 (0.19), residues: 765 sheet: 0.49 (0.78), residues: 57 loop : 0.58 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 367 HIS 0.007 0.001 HIS B 299 PHE 0.010 0.001 PHE A 447 TYR 0.019 0.001 TYR B 366 ARG 0.002 0.000 ARG B 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7539 (t-100) cc_final: 0.7079 (t-100) REVERT: A 242 GLU cc_start: 0.8601 (tm-30) cc_final: 0.8054 (tt0) REVERT: A 285 MET cc_start: 0.7659 (mpp) cc_final: 0.7105 (mpp) REVERT: A 287 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7334 (mmm160) REVERT: A 335 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7397 (tp) REVERT: A 404 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.6977 (tp30) REVERT: A 451 GLN cc_start: 0.8504 (tm-30) cc_final: 0.8159 (tm-30) REVERT: B 401 ASP cc_start: 0.7732 (m-30) cc_final: 0.7496 (t0) REVERT: B 424 GLN cc_start: 0.9048 (tt0) cc_final: 0.8668 (tp40) REVERT: B 586 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7367 (p0) outliers start: 36 outliers final: 30 residues processed: 114 average time/residue: 0.1451 time to fit residues: 25.9028 Evaluate side-chains 113 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 656 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7798 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8001 Z= 0.187 Angle : 0.503 8.459 10884 Z= 0.257 Chirality : 0.037 0.140 1304 Planarity : 0.003 0.045 1421 Dihedral : 3.126 15.175 1183 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 5.03 % Allowed : 27.55 % Favored : 67.41 % 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: 2.76 (0.26), residues: 1107 helix: 2.43 (0.19), residues: 765 sheet: 0.45 (0.77), residues: 57 loop : 0.54 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 367 HIS 0.007 0.001 HIS B 299 PHE 0.012 0.001 PHE A 447 TYR 0.023 0.001 TYR B 366 ARG 0.002 0.000 ARG B 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2214 Ramachandran restraints generated. 1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 214 TRP cc_start: 0.7619 (t-100) cc_final: 0.7184 (t-100) REVERT: A 242 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8057 (tt0) REVERT: A 285 MET cc_start: 0.7723 (mpp) cc_final: 0.7141 (mpp) REVERT: A 287 ARG cc_start: 0.7880 (mmm160) cc_final: 0.7312 (mmm160) REVERT: A 335 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7442 (tp) REVERT: A 404 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7035 (tp30) REVERT: A 451 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8178 (tm-30) REVERT: B 401 ASP cc_start: 0.7744 (m-30) cc_final: 0.7519 (t0) REVERT: B 424 GLN cc_start: 0.9060 (tt0) cc_final: 0.8678 (tp40) REVERT: B 586 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7361 (p0) outliers start: 36 outliers final: 30 residues processed: 112 average time/residue: 0.1402 time to fit residues: 24.3109 Evaluate side-chains 113 residues out of total 945 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 80 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 301 GLU Chi-restraints excluded: chain A residue 314 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 404 GLU Chi-restraints excluded: chain A residue 440 SER Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 478 ILE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 299 HIS Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 437 VAL Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 485 VAL Chi-restraints excluded: chain B residue 498 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 656 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 36 optimal weight: 20.0000 chunk 90 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 0.0010 chunk 63 optimal weight: 0.7980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.135671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.101701 restraints weight = 15519.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.104971 restraints weight = 8175.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.107075 restraints weight = 5511.626| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8001 Z= 0.146 Angle : 0.480 7.975 10884 Z= 0.245 Chirality : 0.036 0.136 1304 Planarity : 0.003 0.046 1421 Dihedral : 3.045 14.794 1183 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.76 % Allowed : 28.11 % Favored : 67.13 % 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: 2.87 (0.26), residues: 1107 helix: 2.50 (0.19), residues: 766 sheet: 0.54 (0.78), residues: 57 loop : 0.60 (0.38), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 367 HIS 0.007 0.001 HIS B 299 PHE 0.011 0.001 PHE A 447 TYR 0.024 0.001 TYR B 366 ARG 0.002 0.000 ARG B 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1676.14 seconds wall clock time: 31 minutes 19.38 seconds (1879.38 seconds total)