Starting phenix.real_space_refine on Tue Dec 31 17:27:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qtz_18655/12_2024/8qtz_18655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qtz_18655/12_2024/8qtz_18655.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qtz_18655/12_2024/8qtz_18655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qtz_18655/12_2024/8qtz_18655.map" model { file = "/net/cci-nas-00/data/ceres_data/8qtz_18655/12_2024/8qtz_18655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qtz_18655/12_2024/8qtz_18655.cif" } resolution = 4.27 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= 0.088 sd= 0.830 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 52 5.16 5 C 10258 2.51 5 N 2726 2.21 5 O 3224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16260 Number of models: 1 Model: "" Number of chains: 3 Chain: "X" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5977 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Chain: "Y" Number of atoms: 5977 Number of conformers: 1 Conformer: "" Number of residues, atoms: 760, 5977 Classifications: {'peptide': 760} Link IDs: {'PTRANS': 34, 'TRANS': 725} Chain breaks: 1 Chain: "Z" Number of atoms: 4306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4306 Classifications: {'peptide': 547} Link IDs: {'PTRANS': 17, 'TRANS': 529} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY X 156 " occ=0.96 ... (2 atoms not shown) pdb=" O GLY X 156 " occ=0.96 Time building chain proxies: 9.28, per 1000 atoms: 0.57 Number of scatterers: 16260 At special positions: 0 Unit cell: (175.89, 175.89, 154.44, 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 52 16.00 O 3224 8.00 N 2726 7.00 C 10258 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: 3.94 Conformation dependent library (CDL) restraints added in 2.2 seconds 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3922 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 27 sheets defined 30.1% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'X' and resid 1 through 12 Processing helix chain 'X' and resid 15 through 26 Processing helix chain 'X' and resid 212 through 222 removed outlier: 3.662A pdb=" N CYS X 216 " --> pdb=" O GLU X 212 " (cutoff:3.500A) Processing helix chain 'X' and resid 359 through 365 Processing helix chain 'X' and resid 494 through 510 removed outlier: 4.053A pdb=" N LEU X 498 " --> pdb=" O LEU X 494 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU X 500 " --> pdb=" O ARG X 496 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLU X 503 " --> pdb=" O GLY X 499 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU X 504 " --> pdb=" O GLU X 500 " (cutoff:3.500A) Processing helix chain 'X' and resid 515 through 523 removed outlier: 3.724A pdb=" N ASP X 519 " --> pdb=" O SER X 515 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU X 522 " --> pdb=" O ILE X 518 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU X 523 " --> pdb=" O ASP X 519 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 533 removed outlier: 3.728A pdb=" N PHE X 531 " --> pdb=" O MET X 527 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLY X 533 " --> pdb=" O SER X 529 " (cutoff:3.500A) Processing helix chain 'X' and resid 543 through 553 Processing helix chain 'X' and resid 555 through 572 removed outlier: 3.638A pdb=" N ASN X 559 " --> pdb=" O SER X 555 " (cutoff:3.500A) Processing helix chain 'X' and resid 594 through 598 removed outlier: 3.643A pdb=" N GLN X 597 " --> pdb=" O VAL X 594 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE X 598 " --> pdb=" O SER X 595 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 594 through 598' Processing helix chain 'X' and resid 606 through 624 removed outlier: 3.996A pdb=" N THR X 610 " --> pdb=" O SER X 606 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN X 611 " --> pdb=" O SER X 607 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG X 618 " --> pdb=" O THR X 614 " (cutoff:3.500A) Processing helix chain 'X' and resid 632 through 646 removed outlier: 3.816A pdb=" N ILE X 636 " --> pdb=" O ASN X 632 " (cutoff:3.500A) Processing helix chain 'X' and resid 655 through 667 removed outlier: 3.928A pdb=" N ILE X 659 " --> pdb=" O THR X 655 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 713 removed outlier: 3.529A pdb=" N LEU X 711 " --> pdb=" O LYS X 707 " (cutoff:3.500A) Processing helix chain 'X' and resid 723 through 731 Processing helix chain 'X' and resid 739 through 744 Processing helix chain 'X' and resid 748 through 759 removed outlier: 4.184A pdb=" N LEU X 752 " --> pdb=" O ASP X 748 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN X 758 " --> pdb=" O GLU X 754 " (cutoff:3.500A) Processing helix chain 'X' and resid 761 through 774 removed outlier: 3.869A pdb=" N ASN X 765 " --> pdb=" O PRO X 761 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 12 Processing helix chain 'Y' and resid 12 through 29 removed outlier: 3.861A pdb=" N ASP Y 17 " --> pdb=" O SER Y 13 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU Y 18 " --> pdb=" O TYR Y 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 120 through 124 Processing helix chain 'Y' and resid 209 through 211 No H-bonds generated for 'chain 'Y' and resid 209 through 211' Processing helix chain 'Y' and resid 212 through 222 Processing helix chain 'Y' and resid 359 through 364 removed outlier: 3.514A pdb=" N ASN Y 364 " --> pdb=" O GLN Y 360 " (cutoff:3.500A) Processing helix chain 'Y' and resid 497 through 510 removed outlier: 3.842A pdb=" N LEU Y 501 " --> pdb=" O GLN Y 497 " (cutoff:3.500A) Processing helix chain 'Y' and resid 514 through 521 Processing helix chain 'Y' and resid 528 through 532 Processing helix chain 'Y' and resid 540 through 553 removed outlier: 4.000A pdb=" N LYS Y 553 " --> pdb=" O MET Y 549 " (cutoff:3.500A) Processing helix chain 'Y' and resid 555 through 574 removed outlier: 3.821A pdb=" N SER Y 574 " --> pdb=" O ASP Y 570 " (cutoff:3.500A) Processing helix chain 'Y' and resid 592 through 597 removed outlier: 3.535A pdb=" N THR Y 596 " --> pdb=" O THR Y 592 " (cutoff:3.500A) Processing helix chain 'Y' and resid 608 through 619 Processing helix chain 'Y' and resid 620 through 625 Processing helix chain 'Y' and resid 632 through 647 removed outlier: 3.816A pdb=" N ILE Y 636 " --> pdb=" O ASN Y 632 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA Y 639 " --> pdb=" O ASP Y 635 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS Y 647 " --> pdb=" O THR Y 643 " (cutoff:3.500A) Processing helix chain 'Y' and resid 652 through 654 No H-bonds generated for 'chain 'Y' and resid 652 through 654' Processing helix chain 'Y' and resid 655 through 667 removed outlier: 4.060A pdb=" N ILE Y 659 " --> pdb=" O THR Y 655 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR Y 661 " --> pdb=" O PRO Y 657 " (cutoff:3.500A) Processing helix chain 'Y' and resid 705 through 713 removed outlier: 3.799A pdb=" N THR Y 713 " --> pdb=" O ALA Y 709 " (cutoff:3.500A) Processing helix chain 'Y' and resid 723 through 734 Processing helix chain 'Y' and resid 737 through 745 Processing helix chain 'Y' and resid 748 through 758 removed outlier: 4.023A pdb=" N LEU Y 752 " --> pdb=" O ASP Y 748 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLN Y 758 " --> pdb=" O GLU Y 754 " (cutoff:3.500A) Processing helix chain 'Y' and resid 762 through 774 Processing helix chain 'Z' and resid 2 through 12 Processing helix chain 'Z' and resid 15 through 26 removed outlier: 3.677A pdb=" N SER Z 19 " --> pdb=" O THR Z 15 " (cutoff:3.500A) Processing helix chain 'Z' and resid 359 through 364 removed outlier: 3.593A pdb=" N ARG Z 363 " --> pdb=" O SER Z 359 " (cutoff:3.500A) Processing helix chain 'Z' and resid 502 through 511 Processing helix chain 'Z' and resid 515 through 521 removed outlier: 3.504A pdb=" N ASP Z 519 " --> pdb=" O SER Z 515 " (cutoff:3.500A) Processing helix chain 'Z' and resid 526 through 531 removed outlier: 3.542A pdb=" N PHE Z 531 " --> pdb=" O MET Z 527 " (cutoff:3.500A) Processing helix chain 'Z' and resid 540 through 552 removed outlier: 4.622A pdb=" N MET Z 549 " --> pdb=" O ALA Z 545 " (cutoff:3.500A) Processing helix chain 'Z' and resid 553 through 555 No H-bonds generated for 'chain 'Z' and resid 553 through 555' Processing helix chain 'Z' and resid 557 through 571 Processing helix chain 'Z' and resid 607 through 624 removed outlier: 3.652A pdb=" N GLN Z 611 " --> pdb=" O SER Z 607 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N MET Z 624 " --> pdb=" O ARG Z 620 " (cutoff:3.500A) Processing helix chain 'Z' and resid 632 through 647 removed outlier: 3.903A pdb=" N ILE Z 636 " --> pdb=" O ASN Z 632 " (cutoff:3.500A) Processing helix chain 'Z' and resid 655 through 667 removed outlier: 4.860A pdb=" N THR Z 661 " --> pdb=" O PRO Z 657 " (cutoff:3.500A) Processing helix chain 'Z' and resid 705 through 714 removed outlier: 4.149A pdb=" N ASP Z 714 " --> pdb=" O ASP Z 710 " (cutoff:3.500A) Processing helix chain 'Z' and resid 723 through 735 Processing helix chain 'Z' and resid 737 through 746 Processing helix chain 'Z' and resid 748 through 759 removed outlier: 3.535A pdb=" N LEU Z 752 " --> pdb=" O ASP Z 748 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN Z 758 " --> pdb=" O GLU Z 754 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ASP Z 759 " --> pdb=" O PHE Z 755 " (cutoff:3.500A) Processing helix chain 'Z' and resid 761 through 774 removed outlier: 3.663A pdb=" N ASN Z 765 " --> pdb=" O PRO Z 761 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS Z 774 " --> pdb=" O LEU Z 770 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'X' and resid 49 through 50 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 49 through 50 current: chain 'X' and resid 402 through 415 removed outlier: 4.999A pdb=" N ARG X 427 " --> pdb=" O ALA X 407 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N VAL X 409 " --> pdb=" O ARG X 425 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG X 425 " --> pdb=" O VAL X 409 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU X 411 " --> pdb=" O SER X 423 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N SER X 423 " --> pdb=" O LEU X 411 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR X 413 " --> pdb=" O LEU X 421 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU X 421 " --> pdb=" O THR X 413 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 420 through 432 current: chain 'Y' and resid 310 through 315 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 310 through 315 current: chain 'Y' and resid 350 through 357 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 350 through 357 current: chain 'Y' and resid 401 through 416 removed outlier: 5.146A pdb=" N LEU Y 404 " --> pdb=" O ALA Y 431 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA Y 431 " --> pdb=" O LEU Y 404 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER Y 406 " --> pdb=" O ARG Y 429 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ARG Y 429 " --> pdb=" O SER Y 406 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY Y 408 " --> pdb=" O ARG Y 427 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 60 through 61 removed outlier: 6.163A pdb=" N THR X 60 " --> pdb=" O ASP Y 325 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N SER Y 327 " --> pdb=" O THR X 60 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N PHE Y 328 " --> pdb=" O SER Y 340 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER Y 340 " --> pdb=" O PHE Y 328 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLY Y 330 " --> pdb=" O VAL Y 338 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N VAL Y 338 " --> pdb=" O GLY Y 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 73 through 74 removed outlier: 4.644A pdb=" N VAL X 93 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR X 105 " --> pdb=" O VAL X 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 80 through 83 removed outlier: 3.555A pdb=" N TYR X 206 " --> pdb=" O LEU X 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 116 through 121 removed outlier: 4.125A pdb=" N ARG X 117 " --> pdb=" O LEU X 128 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU X 128 " --> pdb=" O ARG X 117 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 138 through 140 removed outlier: 3.641A pdb=" N TRP X 138 " --> pdb=" O SER X 160 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 252 through 267 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 252 through 267 current: chain 'X' and resid 469 through 474 WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 469 through 474 current: chain 'Y' and resid 462 through 474 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'X' and resid 270 through 275 Processing sheet with id=AA9, first strand: chain 'X' and resid 279 through 282 removed outlier: 9.066A pdb=" N TRP X 291 " --> pdb=" O SER X 340 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N PHE X 342 " --> pdb=" O TRP X 291 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N GLU X 293 " --> pdb=" O PHE X 342 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N VAL X 344 " --> pdb=" O GLU X 293 " (cutoff:3.500A) removed outlier: 10.414A pdb=" N SER X 295 " --> pdb=" O VAL X 344 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'X' and resid 315 through 317 removed outlier: 3.924A pdb=" N THR X 317 " --> pdb=" O ASP X 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'X' and resid 320 through 321 Processing sheet with id=AB3, first strand: chain 'X' and resid 384 through 386 Processing sheet with id=AB4, first strand: chain 'X' and resid 693 through 694 removed outlier: 3.750A pdb=" N TYR X 693 " --> pdb=" O VAL X 681 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL X 681 " --> pdb=" O TYR X 693 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL X 675 " --> pdb=" O PHE X 682 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 33 through 34 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 33 through 34 current: chain 'Z' and resid 290 through 295 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 290 through 295 current: chain 'Z' and resid 338 through 345 Processing sheet with id=AB6, first strand: chain 'Y' and resid 81 through 82 Processing sheet with id=AB7, first strand: chain 'Y' and resid 95 through 96 removed outlier: 3.932A pdb=" N TRP Y 102 " --> pdb=" O LYS Y 145 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA Y 104 " --> pdb=" O VAL Y 143 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TRP Y 138 " --> pdb=" O LEU Y 159 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU Y 159 " --> pdb=" O TRP Y 138 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N PHE Y 140 " --> pdb=" O SER Y 157 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 115 through 116 removed outlier: 3.554A pdb=" N VAL Y 130 " --> pdb=" O GLU Y 115 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 177 through 178 Processing sheet with id=AC1, first strand: chain 'Y' and resid 278 through 281 removed outlier: 4.010A pdb=" N ALA Y 278 " --> pdb=" O LYS Y 297 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR Y 280 " --> pdb=" O SER Y 295 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 384 through 386 Processing sheet with id=AC3, first strand: chain 'Y' and resid 680 through 685 Processing sheet with id=AC4, first strand: chain 'Z' and resid 263 through 264 removed outlier: 3.573A pdb=" N LYS Z 263 " --> pdb=" O VAL Z 474 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Z' and resid 271 through 273 Processing sheet with id=AC6, first strand: chain 'Z' and resid 300 through 307 removed outlier: 3.616A pdb=" N TYR Z 303 " --> pdb=" O ALA Z 314 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR Z 317 " --> pdb=" O ASP Z 354 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP Z 354 " --> pdb=" O THR Z 317 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL Z 351 " --> pdb=" O PHE Z 428 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE Z 428 " --> pdb=" O VAL Z 351 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LEU Z 421 " --> pdb=" O THR Z 413 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR Z 413 " --> pdb=" O LEU Z 421 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N SER Z 423 " --> pdb=" O LEU Z 411 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N LEU Z 411 " --> pdb=" O SER Z 423 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ARG Z 425 " --> pdb=" O VAL Z 409 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL Z 409 " --> pdb=" O ARG Z 425 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ARG Z 427 " --> pdb=" O ALA Z 407 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS Z 380 " --> pdb=" O VAL Z 402 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 371 through 372 removed outlier: 3.768A pdb=" N ALA Z 372 " --> pdb=" O SER Z 469 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 384 through 386 Processing sheet with id=AC9, first strand: chain 'Z' and resid 690 through 694 removed outlier: 3.867A pdb=" N PHE Z 682 " --> pdb=" O VAL Z 675 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL Z 675 " --> pdb=" O PHE Z 682 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1332 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.88 Time building geometry restraints manager: 4.57 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: 5251 1.34 - 1.46: 2833 1.46 - 1.58: 8406 1.58 - 1.70: 0 1.70 - 1.81: 91 Bond restraints: 16581 Sorted by residual: bond pdb=" N ASP Y 658 " pdb=" CA ASP Y 658 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.88e+00 bond pdb=" N ALA X 541 " pdb=" CA ALA X 541 " ideal model delta sigma weight residual 1.457 1.490 -0.032 1.29e-02 6.01e+03 6.25e+00 bond pdb=" N SER X 543 " pdb=" CA SER X 543 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.13e+00 bond pdb=" N SER Y 3 " pdb=" CA SER Y 3 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.12e+00 bond pdb=" N ILE Y 656 " pdb=" CA ILE Y 656 " ideal model delta sigma weight residual 1.464 1.495 -0.030 1.23e-02 6.61e+03 6.12e+00 ... (remaining 16576 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 21890 2.22 - 4.44: 517 4.44 - 6.66: 98 6.66 - 8.88: 13 8.88 - 11.10: 5 Bond angle restraints: 22523 Sorted by residual: angle pdb=" C ASN Y 97 " pdb=" N ASN Y 98 " pdb=" CA ASN Y 98 " ideal model delta sigma weight residual 121.54 132.24 -10.70 1.91e+00 2.74e-01 3.14e+01 angle pdb=" C ASN X 97 " pdb=" N ASN X 98 " pdb=" CA ASN X 98 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" N VAL X 366 " pdb=" CA VAL X 366 " pdb=" C VAL X 366 " ideal model delta sigma weight residual 112.12 108.02 4.10 8.40e-01 1.42e+00 2.38e+01 angle pdb=" C GLN Z 393 " pdb=" N TRP Z 394 " pdb=" CA TRP Z 394 " ideal model delta sigma weight residual 120.68 128.03 -7.35 1.52e+00 4.33e-01 2.34e+01 angle pdb=" CA PRO Y 657 " pdb=" C PRO Y 657 " pdb=" O PRO Y 657 " ideal model delta sigma weight residual 121.34 116.13 5.21 1.14e+00 7.69e-01 2.09e+01 ... (remaining 22518 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 8989 17.23 - 34.46: 829 34.46 - 51.68: 141 51.68 - 68.91: 23 68.91 - 86.14: 17 Dihedral angle restraints: 9999 sinusoidal: 3935 harmonic: 6064 Sorted by residual: dihedral pdb=" CA ARG Y 210 " pdb=" C ARG Y 210 " pdb=" N SER Y 211 " pdb=" CA SER Y 211 " ideal model delta harmonic sigma weight residual -180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA MET Z 549 " pdb=" C MET Z 549 " pdb=" N LYS Z 550 " pdb=" CA LYS Z 550 " ideal model delta harmonic sigma weight residual 180.00 154.53 25.47 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" C ASP Y 658 " pdb=" N ASP Y 658 " pdb=" CA ASP Y 658 " pdb=" CB ASP Y 658 " ideal model delta harmonic sigma weight residual -122.60 -135.25 12.65 0 2.50e+00 1.60e-01 2.56e+01 ... (remaining 9996 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 2348 0.086 - 0.172: 216 0.172 - 0.258: 8 0.258 - 0.343: 3 0.343 - 0.429: 2 Chirality restraints: 2577 Sorted by residual: chirality pdb=" CA ASP Y 658 " pdb=" N ASP Y 658 " pdb=" C ASP Y 658 " pdb=" CB ASP Y 658 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CB ILE Z 668 " pdb=" CA ILE Z 668 " pdb=" CG1 ILE Z 668 " pdb=" CG2 ILE Z 668 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CB ILE X 55 " pdb=" CA ILE X 55 " pdb=" CG1 ILE X 55 " pdb=" CG2 ILE X 55 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2574 not shown) Planarity restraints: 2917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP X 356 " 0.010 2.00e-02 2.50e+03 1.79e-02 7.99e+00 pdb=" CG TRP X 356 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP X 356 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP X 356 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP X 356 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP X 356 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP X 356 " -0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP X 356 " -0.015 2.00e-02 2.50e+03 pdb=" CZ3 TRP X 356 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP X 356 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP Y 454 " -0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO Y 455 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO Y 455 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO Y 455 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Y 224 " 0.037 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO Y 225 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO Y 225 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO Y 225 " 0.031 5.00e-02 4.00e+02 ... (remaining 2914 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 409 2.63 - 3.20: 16486 3.20 - 3.77: 25866 3.77 - 4.33: 34000 4.33 - 4.90: 52553 Nonbonded interactions: 129314 Sorted by model distance: nonbonded pdb=" OG SER X 257 " pdb=" OE2 GLU Y 264 " model vdw 2.065 3.040 nonbonded pdb=" OG SER Y 583 " pdb=" OE1 GLN Y 597 " model vdw 2.099 3.040 nonbonded pdb=" OG SER Y 160 " pdb=" OH TYR Y 165 " model vdw 2.128 3.040 nonbonded pdb=" OG SER Y 586 " pdb=" OE1 GLN Y 706 " model vdw 2.149 3.040 nonbonded pdb=" O SER Z 292 " pdb=" OG SER Z 340 " model vdw 2.151 3.040 ... (remaining 129309 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 Found NCS groups: ncs_group { reference = chain 'X' selection = chain 'Y' } 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=0.00 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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.630 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 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:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 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 : 0.004 0.046 16581 Z= 0.243 Angle : 0.863 11.101 22523 Z= 0.479 Chirality : 0.050 0.429 2577 Planarity : 0.005 0.068 2917 Dihedral : 13.806 86.141 6077 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.00 % Favored : 88.66 % Rotamer: Outliers : 0.05 % Allowed : 0.38 % Favored : 99.56 % Cbeta Deviations : 0.05 % 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: -3.58 (0.17), residues: 2055 helix: -1.04 (0.21), residues: 525 sheet: -1.74 (0.23), residues: 483 loop : -3.52 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP X 356 HIS 0.002 0.001 HIS Y 188 PHE 0.029 0.002 PHE Y 505 TYR 0.026 0.002 TYR X 219 ARG 0.008 0.001 ARG Y 446 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 610 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 23 GLN cc_start: 0.8818 (mm110) cc_final: 0.8506 (tp-100) REVERT: X 25 ILE cc_start: 0.9111 (tp) cc_final: 0.8799 (tp) REVERT: X 31 GLN cc_start: 0.7421 (tm-30) cc_final: 0.6607 (tm-30) REVERT: X 33 VAL cc_start: 0.7539 (t) cc_final: 0.6929 (p) REVERT: X 81 TRP cc_start: 0.6931 (m100) cc_final: 0.5851 (m100) REVERT: X 140 PHE cc_start: 0.7319 (t80) cc_final: 0.6985 (t80) REVERT: X 224 LEU cc_start: 0.8331 (tt) cc_final: 0.7992 (tt) REVERT: X 263 LYS cc_start: 0.8088 (tptt) cc_final: 0.7642 (ttmt) REVERT: X 321 ASN cc_start: 0.8145 (t0) cc_final: 0.7732 (t0) REVERT: X 367 TYR cc_start: 0.8138 (m-80) cc_final: 0.7643 (m-80) REVERT: X 375 LEU cc_start: 0.8945 (mm) cc_final: 0.8683 (mt) REVERT: X 512 ILE cc_start: 0.9218 (mm) cc_final: 0.8924 (mm) REVERT: X 575 ILE cc_start: 0.9369 (mm) cc_final: 0.8970 (mp) REVERT: X 634 ASP cc_start: 0.8670 (m-30) cc_final: 0.8461 (m-30) REVERT: X 687 ASP cc_start: 0.8218 (m-30) cc_final: 0.8016 (t0) REVERT: X 699 GLU cc_start: 0.8338 (mp0) cc_final: 0.7457 (mp0) REVERT: X 710 ASP cc_start: 0.8215 (p0) cc_final: 0.7847 (m-30) REVERT: X 718 ILE cc_start: 0.8856 (tp) cc_final: 0.8526 (tp) REVERT: X 729 ASN cc_start: 0.9071 (t0) cc_final: 0.8832 (t0) REVERT: X 770 LEU cc_start: 0.9079 (tt) cc_final: 0.8702 (tp) REVERT: X 773 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8064 (tm-30) REVERT: Y 258 LYS cc_start: 0.9131 (mmmt) cc_final: 0.8869 (mmmm) REVERT: Y 271 ILE cc_start: 0.8830 (mm) cc_final: 0.8011 (mm) REVERT: Y 273 ILE cc_start: 0.8635 (tp) cc_final: 0.8292 (tp) REVERT: Y 328 PHE cc_start: 0.8680 (t80) cc_final: 0.8413 (t80) REVERT: Y 367 TYR cc_start: 0.8547 (m-80) cc_final: 0.8221 (m-80) REVERT: Y 460 GLU cc_start: 0.7938 (tp30) cc_final: 0.7734 (tp30) REVERT: Y 530 MET cc_start: 0.8873 (tpt) cc_final: 0.8587 (tpp) REVERT: Y 549 MET cc_start: 0.7879 (mtm) cc_final: 0.7532 (mmm) REVERT: Y 596 THR cc_start: 0.8620 (p) cc_final: 0.8404 (p) REVERT: Y 634 ASP cc_start: 0.7797 (p0) cc_final: 0.7050 (p0) REVERT: Y 643 THR cc_start: 0.9302 (m) cc_final: 0.8955 (t) REVERT: Y 645 ILE cc_start: 0.8878 (pt) cc_final: 0.8656 (pt) REVERT: Y 662 GLU cc_start: 0.8849 (pt0) cc_final: 0.8516 (pt0) REVERT: Y 673 TYR cc_start: 0.7905 (m-80) cc_final: 0.7602 (m-80) REVERT: Y 727 LEU cc_start: 0.9095 (mt) cc_final: 0.8877 (mt) REVERT: Y 743 ASN cc_start: 0.8984 (m-40) cc_final: 0.8667 (m-40) REVERT: Y 744 LEU cc_start: 0.9428 (mm) cc_final: 0.9048 (mm) REVERT: Y 753 ARG cc_start: 0.8065 (mtp-110) cc_final: 0.7769 (ttt90) REVERT: Y 765 ASN cc_start: 0.8319 (t0) cc_final: 0.8067 (t0) REVERT: Y 769 GLN cc_start: 0.7318 (mm110) cc_final: 0.6701 (mm110) REVERT: Y 773 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8440 (tm-30) REVERT: Z 1 MET cc_start: 0.8723 (tmm) cc_final: 0.8367 (tmm) REVERT: Z 271 ILE cc_start: 0.9287 (tp) cc_final: 0.8685 (tp) REVERT: Z 352 TYR cc_start: 0.8005 (m-10) cc_final: 0.7727 (m-80) REVERT: Z 422 ASN cc_start: 0.8304 (p0) cc_final: 0.8015 (p0) REVERT: Z 494 LEU cc_start: 0.8489 (mp) cc_final: 0.8190 (tt) REVERT: Z 505 PHE cc_start: 0.8186 (m-80) cc_final: 0.7528 (m-80) REVERT: Z 525 LEU cc_start: 0.8748 (pt) cc_final: 0.8428 (pp) REVERT: Z 611 GLN cc_start: 0.8767 (mp10) cc_final: 0.8395 (mp10) REVERT: Z 631 MET cc_start: 0.8215 (tmm) cc_final: 0.7863 (tmm) REVERT: Z 632 ASN cc_start: 0.8299 (t0) cc_final: 0.7503 (p0) REVERT: Z 643 THR cc_start: 0.8446 (p) cc_final: 0.8147 (p) REVERT: Z 644 LYS cc_start: 0.8507 (mmtp) cc_final: 0.8234 (mttm) REVERT: Z 659 ILE cc_start: 0.8907 (mm) cc_final: 0.8644 (tp) REVERT: Z 666 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8512 (mmmm) REVERT: Z 676 ILE cc_start: 0.8888 (mm) cc_final: 0.8617 (tp) REVERT: Z 682 PHE cc_start: 0.7559 (p90) cc_final: 0.7023 (p90) REVERT: Z 683 GLU cc_start: 0.7692 (pp20) cc_final: 0.7399 (pm20) REVERT: Z 714 ASP cc_start: 0.8386 (t0) cc_final: 0.8056 (t0) REVERT: Z 721 ILE cc_start: 0.9135 (mt) cc_final: 0.8457 (mt) REVERT: Z 728 LYS cc_start: 0.6037 (ttpt) cc_final: 0.5787 (tppt) REVERT: Z 739 GLN cc_start: 0.8097 (tp-100) cc_final: 0.6794 (tp40) REVERT: Z 748 ASP cc_start: 0.8928 (t0) cc_final: 0.8708 (t0) REVERT: Z 754 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8397 (tm-30) outliers start: 1 outliers final: 0 residues processed: 610 average time/residue: 0.3105 time to fit residues: 271.9145 Evaluate side-chains 494 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 161 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 98 optimal weight: 0.0000 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 559 ASN X 757 ASN ** Y 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 678 ASN Y 731 ASN Z 678 ASN Z 739 GLN ** Z 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16581 Z= 0.312 Angle : 0.787 10.411 22523 Z= 0.412 Chirality : 0.049 0.254 2577 Planarity : 0.006 0.063 2917 Dihedral : 6.038 26.829 2239 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 18.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 12.12 % Favored : 87.69 % Rotamer: Outliers : 0.54 % Allowed : 6.81 % Favored : 92.65 % 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: -3.61 (0.17), residues: 2055 helix: -1.13 (0.20), residues: 544 sheet: -1.64 (0.24), residues: 441 loop : -3.55 (0.16), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP X 356 HIS 0.002 0.001 HIS Y 170 PHE 0.041 0.002 PHE X 505 TYR 0.029 0.002 TYR Z 305 ARG 0.006 0.001 ARG Z 369 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 526 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8881 (p0) cc_final: 0.8669 (p0) REVERT: X 81 TRP cc_start: 0.7264 (m100) cc_final: 0.5801 (m100) REVERT: X 263 LYS cc_start: 0.8390 (tptt) cc_final: 0.7934 (ttmt) REVERT: X 341 LYS cc_start: 0.7908 (tptt) cc_final: 0.7689 (tppt) REVERT: X 367 TYR cc_start: 0.8457 (m-80) cc_final: 0.7828 (m-80) REVERT: X 414 GLN cc_start: 0.8753 (tp40) cc_final: 0.8529 (tp40) REVERT: X 423 SER cc_start: 0.9196 (t) cc_final: 0.8961 (p) REVERT: X 512 ILE cc_start: 0.9151 (mm) cc_final: 0.8924 (mm) REVERT: X 530 MET cc_start: 0.8709 (ttp) cc_final: 0.8379 (ttp) REVERT: X 531 PHE cc_start: 0.9143 (m-10) cc_final: 0.8572 (m-10) REVERT: X 551 LYS cc_start: 0.9116 (ttmt) cc_final: 0.8720 (ttpt) REVERT: X 575 ILE cc_start: 0.9382 (mm) cc_final: 0.8943 (mp) REVERT: X 635 ASP cc_start: 0.8913 (m-30) cc_final: 0.8639 (m-30) REVERT: X 662 GLU cc_start: 0.8424 (pt0) cc_final: 0.7915 (pt0) REVERT: X 666 LYS cc_start: 0.9230 (mtmm) cc_final: 0.8792 (mtmm) REVERT: X 694 LYS cc_start: 0.8581 (tptp) cc_final: 0.8180 (tptt) REVERT: X 699 GLU cc_start: 0.7975 (mp0) cc_final: 0.7722 (mp0) REVERT: X 707 LYS cc_start: 0.8796 (tptp) cc_final: 0.8316 (tptp) REVERT: X 713 THR cc_start: 0.9283 (t) cc_final: 0.8933 (t) REVERT: X 718 ILE cc_start: 0.9073 (tp) cc_final: 0.8556 (tp) REVERT: X 729 ASN cc_start: 0.9172 (t0) cc_final: 0.8962 (t0) REVERT: X 762 ILE cc_start: 0.8518 (pt) cc_final: 0.8234 (pt) REVERT: X 773 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8278 (tm-30) REVERT: Y 17 ASP cc_start: 0.8795 (p0) cc_final: 0.8336 (p0) REVERT: Y 107 LEU cc_start: 0.8630 (tp) cc_final: 0.7787 (tp) REVERT: Y 271 ILE cc_start: 0.8791 (mm) cc_final: 0.8168 (mm) REVERT: Y 328 PHE cc_start: 0.8414 (t80) cc_final: 0.8167 (t80) REVERT: Y 337 PHE cc_start: 0.7997 (m-80) cc_final: 0.7550 (m-80) REVERT: Y 415 PHE cc_start: 0.7802 (t80) cc_final: 0.7138 (t80) REVERT: Y 527 MET cc_start: 0.8521 (ppp) cc_final: 0.8188 (ppp) REVERT: Y 539 ASP cc_start: 0.8050 (t70) cc_final: 0.7725 (t70) REVERT: Y 549 MET cc_start: 0.8147 (mtm) cc_final: 0.7715 (mmm) REVERT: Y 566 ASP cc_start: 0.8320 (p0) cc_final: 0.8098 (p0) REVERT: Y 619 LEU cc_start: 0.8741 (mm) cc_final: 0.8104 (tp) REVERT: Y 634 ASP cc_start: 0.8028 (p0) cc_final: 0.7283 (p0) REVERT: Y 645 ILE cc_start: 0.8911 (pt) cc_final: 0.8694 (pt) REVERT: Y 662 GLU cc_start: 0.8959 (pt0) cc_final: 0.8531 (pt0) REVERT: Y 673 TYR cc_start: 0.8292 (m-80) cc_final: 0.7722 (m-10) REVERT: Y 691 PHE cc_start: 0.8840 (m-80) cc_final: 0.8178 (m-80) REVERT: Y 743 ASN cc_start: 0.9087 (m-40) cc_final: 0.8731 (m-40) REVERT: Y 745 LEU cc_start: 0.9520 (mt) cc_final: 0.9217 (mm) REVERT: Y 769 GLN cc_start: 0.7391 (mm110) cc_final: 0.7015 (tp40) REVERT: Y 773 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8481 (tm-30) REVERT: Z 1 MET cc_start: 0.8609 (tmm) cc_final: 0.8046 (tmm) REVERT: Z 5 ILE cc_start: 0.6922 (mm) cc_final: 0.6115 (mm) REVERT: Z 271 ILE cc_start: 0.9291 (tp) cc_final: 0.8569 (tp) REVERT: Z 356 TRP cc_start: 0.7465 (t-100) cc_final: 0.6494 (t-100) REVERT: Z 422 ASN cc_start: 0.8667 (p0) cc_final: 0.8346 (p0) REVERT: Z 454 ASP cc_start: 0.9037 (t70) cc_final: 0.8763 (t0) REVERT: Z 494 LEU cc_start: 0.8419 (mp) cc_final: 0.8187 (tt) REVERT: Z 505 PHE cc_start: 0.8445 (m-80) cc_final: 0.7566 (m-80) REVERT: Z 611 GLN cc_start: 0.8951 (mp10) cc_final: 0.8372 (mp10) REVERT: Z 623 GLU cc_start: 0.7999 (tp30) cc_final: 0.7233 (mm-30) REVERT: Z 632 ASN cc_start: 0.8521 (t0) cc_final: 0.7906 (t0) REVERT: Z 659 ILE cc_start: 0.9008 (mm) cc_final: 0.8736 (tp) REVERT: Z 674 ARG cc_start: 0.8309 (mtm-85) cc_final: 0.7999 (mtm-85) REVERT: Z 689 LYS cc_start: 0.9211 (mmtm) cc_final: 0.8911 (mmmm) REVERT: Z 728 LYS cc_start: 0.6272 (ttpt) cc_final: 0.5930 (tppt) REVERT: Z 740 GLN cc_start: 0.9003 (mt0) cc_final: 0.8736 (mt0) REVERT: Z 748 ASP cc_start: 0.9048 (t0) cc_final: 0.8787 (t0) REVERT: Z 754 GLU cc_start: 0.8736 (tm-30) cc_final: 0.8474 (tm-30) REVERT: Z 759 ASP cc_start: 0.8757 (p0) cc_final: 0.8460 (p0) REVERT: Z 764 ARG cc_start: 0.8084 (tpm170) cc_final: 0.6984 (tpm170) REVERT: Z 767 ILE cc_start: 0.9102 (tt) cc_final: 0.8324 (tt) outliers start: 10 outliers final: 2 residues processed: 533 average time/residue: 0.3243 time to fit residues: 247.2776 Evaluate side-chains 442 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 440 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 127 optimal weight: 0.0970 chunk 51 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 202 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 63 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 677 ASN Z 773 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16581 Z= 0.225 Angle : 0.742 10.288 22523 Z= 0.386 Chirality : 0.048 0.246 2577 Planarity : 0.005 0.063 2917 Dihedral : 5.866 24.083 2239 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.85 % Favored : 88.95 % Rotamer: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % 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: -3.56 (0.17), residues: 2055 helix: -1.07 (0.20), residues: 545 sheet: -1.73 (0.24), residues: 430 loop : -3.46 (0.16), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 356 HIS 0.003 0.001 HIS Y 436 PHE 0.040 0.002 PHE X 505 TYR 0.030 0.002 TYR Y 461 ARG 0.006 0.000 ARG X 753 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 526 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8878 (p0) cc_final: 0.8637 (p0) REVERT: X 140 PHE cc_start: 0.7601 (t80) cc_final: 0.7022 (t80) REVERT: X 141 ILE cc_start: 0.8655 (pt) cc_final: 0.8424 (pt) REVERT: X 263 LYS cc_start: 0.8356 (tptt) cc_final: 0.7903 (ttmt) REVERT: X 276 LYS cc_start: 0.8554 (tptp) cc_final: 0.8263 (tttt) REVERT: X 341 LYS cc_start: 0.7524 (tptt) cc_final: 0.7254 (tppt) REVERT: X 367 TYR cc_start: 0.8544 (m-80) cc_final: 0.7766 (m-80) REVERT: X 371 LEU cc_start: 0.7807 (pt) cc_final: 0.7366 (pt) REVERT: X 423 SER cc_start: 0.9073 (t) cc_final: 0.8797 (p) REVERT: X 512 ILE cc_start: 0.9183 (mm) cc_final: 0.8948 (mm) REVERT: X 530 MET cc_start: 0.8371 (ttp) cc_final: 0.8171 (ttm) REVERT: X 531 PHE cc_start: 0.9202 (m-10) cc_final: 0.8568 (m-10) REVERT: X 551 LYS cc_start: 0.9140 (ttmt) cc_final: 0.8747 (ttpt) REVERT: X 575 ILE cc_start: 0.9373 (mm) cc_final: 0.8929 (mp) REVERT: X 631 MET cc_start: 0.8683 (tpp) cc_final: 0.8250 (tpp) REVERT: X 635 ASP cc_start: 0.8914 (m-30) cc_final: 0.8258 (m-30) REVERT: X 658 ASP cc_start: 0.8173 (p0) cc_final: 0.7697 (p0) REVERT: X 662 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7305 (pm20) REVERT: X 665 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8637 (tm-30) REVERT: X 666 LYS cc_start: 0.9179 (mtmm) cc_final: 0.8661 (mtmm) REVERT: X 693 TYR cc_start: 0.5772 (t80) cc_final: 0.5059 (t80) REVERT: X 694 LYS cc_start: 0.8565 (tptp) cc_final: 0.8123 (tptt) REVERT: X 699 GLU cc_start: 0.8056 (mp0) cc_final: 0.7776 (mp0) REVERT: X 718 ILE cc_start: 0.8925 (tp) cc_final: 0.8622 (tp) REVERT: X 729 ASN cc_start: 0.9127 (t0) cc_final: 0.8907 (t0) REVERT: X 762 ILE cc_start: 0.8353 (pt) cc_final: 0.8029 (pt) REVERT: X 773 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8200 (tm-30) REVERT: Y 12 ASN cc_start: 0.8101 (m-40) cc_final: 0.7858 (m-40) REVERT: Y 17 ASP cc_start: 0.8819 (p0) cc_final: 0.8429 (p0) REVERT: Y 29 LYS cc_start: 0.8713 (mmpt) cc_final: 0.8466 (tttt) REVERT: Y 107 LEU cc_start: 0.8617 (tp) cc_final: 0.7804 (tp) REVERT: Y 220 ILE cc_start: 0.7526 (tp) cc_final: 0.7181 (pt) REVERT: Y 271 ILE cc_start: 0.8659 (mm) cc_final: 0.8328 (mm) REVERT: Y 273 ILE cc_start: 0.8560 (tp) cc_final: 0.8084 (tp) REVERT: Y 328 PHE cc_start: 0.8500 (t80) cc_final: 0.8252 (t80) REVERT: Y 337 PHE cc_start: 0.7882 (m-80) cc_final: 0.7478 (m-80) REVERT: Y 380 CYS cc_start: 0.8441 (m) cc_final: 0.7837 (t) REVERT: Y 415 PHE cc_start: 0.7588 (t80) cc_final: 0.7024 (t80) REVERT: Y 522 LEU cc_start: 0.9205 (tp) cc_final: 0.8973 (tp) REVERT: Y 527 MET cc_start: 0.8461 (ppp) cc_final: 0.8175 (ppp) REVERT: Y 539 ASP cc_start: 0.8058 (t70) cc_final: 0.7678 (t70) REVERT: Y 549 MET cc_start: 0.8021 (mtm) cc_final: 0.7421 (mmm) REVERT: Y 619 LEU cc_start: 0.8758 (mm) cc_final: 0.8300 (tp) REVERT: Y 634 ASP cc_start: 0.8086 (p0) cc_final: 0.7357 (p0) REVERT: Y 645 ILE cc_start: 0.8887 (pt) cc_final: 0.8642 (pt) REVERT: Y 662 GLU cc_start: 0.8939 (pt0) cc_final: 0.8320 (pt0) REVERT: Y 673 TYR cc_start: 0.8117 (m-80) cc_final: 0.7452 (m-80) REVERT: Y 691 PHE cc_start: 0.8589 (m-80) cc_final: 0.8347 (m-80) REVERT: Y 707 LYS cc_start: 0.9310 (mmmm) cc_final: 0.9095 (mmmm) REVERT: Y 753 ARG cc_start: 0.8094 (ttt90) cc_final: 0.7884 (ttt90) REVERT: Y 769 GLN cc_start: 0.7405 (mm110) cc_final: 0.7024 (tp40) REVERT: Y 773 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8386 (tm-30) REVERT: Z 1 MET cc_start: 0.8787 (tmm) cc_final: 0.8093 (tmm) REVERT: Z 5 ILE cc_start: 0.6903 (mm) cc_final: 0.6168 (mt) REVERT: Z 356 TRP cc_start: 0.7254 (t-100) cc_final: 0.6357 (t-100) REVERT: Z 422 ASN cc_start: 0.8584 (p0) cc_final: 0.8281 (p0) REVERT: Z 581 ILE cc_start: 0.9128 (pt) cc_final: 0.8451 (pt) REVERT: Z 611 GLN cc_start: 0.8916 (mp10) cc_final: 0.8416 (mp10) REVERT: Z 620 ARG cc_start: 0.8157 (tmt170) cc_final: 0.7941 (tpt90) REVERT: Z 623 GLU cc_start: 0.7766 (tp30) cc_final: 0.6975 (tp30) REVERT: Z 624 MET cc_start: 0.7922 (ptp) cc_final: 0.6499 (ptp) REVERT: Z 631 MET cc_start: 0.8202 (tmm) cc_final: 0.7902 (tmm) REVERT: Z 632 ASN cc_start: 0.8600 (t0) cc_final: 0.8162 (t0) REVERT: Z 659 ILE cc_start: 0.9002 (mm) cc_final: 0.8681 (tp) REVERT: Z 666 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8766 (mppt) REVERT: Z 689 LYS cc_start: 0.9157 (mmtm) cc_final: 0.8899 (mmmm) REVERT: Z 718 ILE cc_start: 0.9159 (mp) cc_final: 0.8892 (mp) REVERT: Z 721 ILE cc_start: 0.9377 (mt) cc_final: 0.8830 (mt) REVERT: Z 728 LYS cc_start: 0.6204 (ttpt) cc_final: 0.5822 (tppt) REVERT: Z 748 ASP cc_start: 0.9010 (t0) cc_final: 0.8755 (t0) REVERT: Z 754 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8414 (tm-30) REVERT: Z 759 ASP cc_start: 0.8642 (p0) cc_final: 0.8361 (p0) REVERT: Z 764 ARG cc_start: 0.8071 (tpm170) cc_final: 0.6918 (tpm170) REVERT: Z 767 ILE cc_start: 0.9112 (tt) cc_final: 0.8448 (tt) outliers start: 2 outliers final: 0 residues processed: 527 average time/residue: 0.3080 time to fit residues: 234.0733 Evaluate side-chains 452 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 451 time to evaluate : 1.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 0.9990 chunk 140 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 188 optimal weight: 0.0980 chunk 199 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 178 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 324 ASN ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 760 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16581 Z= 0.201 Angle : 0.727 10.081 22523 Z= 0.374 Chirality : 0.048 0.212 2577 Planarity : 0.005 0.084 2917 Dihedral : 5.655 24.404 2239 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.90 % Favored : 88.91 % Rotamer: Outliers : 0.05 % Allowed : 4.25 % Favored : 95.70 % 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: -3.42 (0.17), residues: 2055 helix: -0.99 (0.21), residues: 544 sheet: -1.57 (0.24), residues: 447 loop : -3.41 (0.17), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 356 HIS 0.002 0.001 HIS X 170 PHE 0.048 0.002 PHE X 505 TYR 0.022 0.001 TYR Z 461 ARG 0.008 0.001 ARG Z 502 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 522 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 14 TYR cc_start: 0.7365 (p90) cc_final: 0.7034 (p90) REVERT: X 20 ASP cc_start: 0.8813 (p0) cc_final: 0.8569 (p0) REVERT: X 25 ILE cc_start: 0.8644 (tp) cc_final: 0.8392 (tp) REVERT: X 81 TRP cc_start: 0.7087 (m100) cc_final: 0.5507 (m100) REVERT: X 140 PHE cc_start: 0.7195 (t80) cc_final: 0.6797 (t80) REVERT: X 141 ILE cc_start: 0.8542 (pt) cc_final: 0.8331 (pt) REVERT: X 142 ASP cc_start: 0.5757 (m-30) cc_final: 0.4970 (m-30) REVERT: X 168 MET cc_start: 0.7798 (pmm) cc_final: 0.7407 (pmm) REVERT: X 263 LYS cc_start: 0.8283 (tptt) cc_final: 0.7958 (ttmt) REVERT: X 273 ILE cc_start: 0.8924 (pt) cc_final: 0.8722 (tt) REVERT: X 355 TYR cc_start: 0.8663 (t80) cc_final: 0.8261 (t80) REVERT: X 367 TYR cc_start: 0.8497 (m-80) cc_final: 0.7783 (m-80) REVERT: X 371 LEU cc_start: 0.7511 (pt) cc_final: 0.6905 (pt) REVERT: X 423 SER cc_start: 0.9131 (t) cc_final: 0.8868 (p) REVERT: X 527 MET cc_start: 0.6904 (mtt) cc_final: 0.6655 (mtt) REVERT: X 530 MET cc_start: 0.8332 (ttp) cc_final: 0.8125 (ttm) REVERT: X 531 PHE cc_start: 0.9183 (m-10) cc_final: 0.8536 (m-10) REVERT: X 551 LYS cc_start: 0.9022 (ttmt) cc_final: 0.8736 (ttpt) REVERT: X 618 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7582 (ptm-80) REVERT: X 635 ASP cc_start: 0.8881 (m-30) cc_final: 0.8035 (m-30) REVERT: X 644 LYS cc_start: 0.8653 (tppt) cc_final: 0.8394 (mmmm) REVERT: X 662 GLU cc_start: 0.8207 (pm20) cc_final: 0.7611 (pm20) REVERT: X 665 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8535 (tm-30) REVERT: X 666 LYS cc_start: 0.9133 (mtmm) cc_final: 0.8535 (mtmm) REVERT: X 694 LYS cc_start: 0.8566 (tptp) cc_final: 0.8150 (tptt) REVERT: X 699 GLU cc_start: 0.8049 (mp0) cc_final: 0.7699 (mp0) REVERT: X 704 ASP cc_start: 0.8489 (t70) cc_final: 0.8251 (t0) REVERT: X 707 LYS cc_start: 0.8825 (tptp) cc_final: 0.8545 (tptp) REVERT: X 718 ILE cc_start: 0.8858 (tp) cc_final: 0.8353 (tp) REVERT: X 773 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8362 (tm-30) REVERT: Y 17 ASP cc_start: 0.8867 (p0) cc_final: 0.8506 (p0) REVERT: Y 42 GLN cc_start: 0.9011 (mp10) cc_final: 0.8666 (mp10) REVERT: Y 69 TYR cc_start: 0.6361 (m-80) cc_final: 0.5402 (m-80) REVERT: Y 107 LEU cc_start: 0.8618 (tp) cc_final: 0.7867 (tp) REVERT: Y 220 ILE cc_start: 0.7428 (tp) cc_final: 0.7085 (pt) REVERT: Y 328 PHE cc_start: 0.8486 (t80) cc_final: 0.8239 (t80) REVERT: Y 380 CYS cc_start: 0.8450 (m) cc_final: 0.7836 (t) REVERT: Y 415 PHE cc_start: 0.7591 (t80) cc_final: 0.6990 (t80) REVERT: Y 500 GLU cc_start: 0.7227 (pt0) cc_final: 0.6169 (pp20) REVERT: Y 522 LEU cc_start: 0.9197 (tp) cc_final: 0.8965 (tp) REVERT: Y 527 MET cc_start: 0.8451 (ppp) cc_final: 0.8178 (ppp) REVERT: Y 539 ASP cc_start: 0.8105 (t70) cc_final: 0.7760 (t0) REVERT: Y 549 MET cc_start: 0.7967 (mtm) cc_final: 0.7355 (mmm) REVERT: Y 619 LEU cc_start: 0.8760 (mm) cc_final: 0.8295 (tp) REVERT: Y 634 ASP cc_start: 0.7762 (p0) cc_final: 0.7183 (p0) REVERT: Y 662 GLU cc_start: 0.8930 (pt0) cc_final: 0.8240 (pt0) REVERT: Y 666 LYS cc_start: 0.8979 (mtmm) cc_final: 0.8718 (mtmm) REVERT: Y 673 TYR cc_start: 0.8187 (m-80) cc_final: 0.7610 (m-80) REVERT: Y 691 PHE cc_start: 0.8850 (m-80) cc_final: 0.8070 (m-80) REVERT: Y 753 ARG cc_start: 0.7857 (ttt90) cc_final: 0.7484 (ttt90) REVERT: Y 769 GLN cc_start: 0.7391 (mm110) cc_final: 0.7049 (tp40) REVERT: Y 773 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8303 (tm-30) REVERT: Z 1 MET cc_start: 0.8778 (tmm) cc_final: 0.8220 (tmm) REVERT: Z 5 ILE cc_start: 0.6761 (mm) cc_final: 0.6058 (mt) REVERT: Z 8 GLN cc_start: 0.7655 (pm20) cc_final: 0.7418 (pm20) REVERT: Z 271 ILE cc_start: 0.9357 (tp) cc_final: 0.8728 (tp) REVERT: Z 356 TRP cc_start: 0.7170 (t-100) cc_final: 0.6533 (t-100) REVERT: Z 494 LEU cc_start: 0.8444 (mp) cc_final: 0.8160 (tt) REVERT: Z 497 GLN cc_start: 0.7695 (mp10) cc_final: 0.7247 (mp10) REVERT: Z 505 PHE cc_start: 0.8537 (m-80) cc_final: 0.7951 (m-80) REVERT: Z 611 GLN cc_start: 0.8926 (mp10) cc_final: 0.8365 (mp10) REVERT: Z 617 ARG cc_start: 0.8643 (ttm110) cc_final: 0.8289 (ttm110) REVERT: Z 623 GLU cc_start: 0.7778 (tp30) cc_final: 0.6870 (mm-30) REVERT: Z 631 MET cc_start: 0.8184 (tmm) cc_final: 0.7880 (tmm) REVERT: Z 632 ASN cc_start: 0.8600 (t0) cc_final: 0.7683 (p0) REVERT: Z 659 ILE cc_start: 0.8919 (mm) cc_final: 0.8593 (tp) REVERT: Z 683 GLU cc_start: 0.7662 (pp20) cc_final: 0.7155 (pp20) REVERT: Z 689 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8830 (mmmm) REVERT: Z 721 ILE cc_start: 0.9425 (mt) cc_final: 0.8856 (mt) REVERT: Z 728 LYS cc_start: 0.6178 (ttpt) cc_final: 0.5794 (tppt) REVERT: Z 748 ASP cc_start: 0.9017 (t0) cc_final: 0.8645 (t70) REVERT: Z 754 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8380 (tm-30) REVERT: Z 759 ASP cc_start: 0.8619 (p0) cc_final: 0.8068 (p0) REVERT: Z 764 ARG cc_start: 0.7860 (tpm170) cc_final: 0.7529 (tpm170) REVERT: Z 767 ILE cc_start: 0.9059 (tt) cc_final: 0.8713 (tt) outliers start: 1 outliers final: 0 residues processed: 523 average time/residue: 0.3132 time to fit residues: 237.6516 Evaluate side-chains 444 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 6.9990 chunk 113 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 169 optimal weight: 5.9990 chunk 137 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 101 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 8 GLN X 611 GLN X 757 ASN ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 477 ASN Z 760 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16581 Z= 0.205 Angle : 0.735 11.657 22523 Z= 0.375 Chirality : 0.047 0.215 2577 Planarity : 0.005 0.071 2917 Dihedral : 5.596 25.525 2239 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.51 % Favored : 89.34 % Rotamer: Outliers : 0.16 % Allowed : 3.05 % Favored : 96.79 % 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: -3.32 (0.17), residues: 2055 helix: -0.99 (0.21), residues: 546 sheet: -1.41 (0.23), residues: 484 loop : -3.39 (0.17), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP X 356 HIS 0.002 0.001 HIS X 170 PHE 0.032 0.002 PHE Y 505 TYR 0.024 0.001 TYR Z 461 ARG 0.005 0.000 ARG Z 502 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 510 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8863 (p0) cc_final: 0.8593 (p0) REVERT: X 25 ILE cc_start: 0.8670 (tp) cc_final: 0.8409 (tp) REVERT: X 140 PHE cc_start: 0.7161 (t80) cc_final: 0.6773 (t80) REVERT: X 142 ASP cc_start: 0.5727 (m-30) cc_final: 0.4843 (m-30) REVERT: X 263 LYS cc_start: 0.8307 (tptt) cc_final: 0.8014 (ttmt) REVERT: X 355 TYR cc_start: 0.8554 (t80) cc_final: 0.8206 (t80) REVERT: X 356 TRP cc_start: 0.5626 (m-10) cc_final: 0.4708 (m-10) REVERT: X 371 LEU cc_start: 0.7586 (pt) cc_final: 0.7101 (pt) REVERT: X 423 SER cc_start: 0.9147 (t) cc_final: 0.8883 (p) REVERT: X 508 LEU cc_start: 0.9437 (pp) cc_final: 0.9057 (pp) REVERT: X 512 ILE cc_start: 0.9328 (mm) cc_final: 0.9053 (mm) REVERT: X 544 MET cc_start: 0.8952 (ppp) cc_final: 0.8242 (ppp) REVERT: X 615 ILE cc_start: 0.9098 (pt) cc_final: 0.8660 (pt) REVERT: X 619 LEU cc_start: 0.8392 (pp) cc_final: 0.8088 (pp) REVERT: X 645 ILE cc_start: 0.9275 (tp) cc_final: 0.8942 (pt) REVERT: X 658 ASP cc_start: 0.8236 (p0) cc_final: 0.7954 (p0) REVERT: X 662 GLU cc_start: 0.8143 (pm20) cc_final: 0.7589 (pm20) REVERT: X 665 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8566 (tm-30) REVERT: X 666 LYS cc_start: 0.9145 (mtmm) cc_final: 0.8562 (mtmm) REVERT: X 694 LYS cc_start: 0.8554 (tptp) cc_final: 0.8130 (tptt) REVERT: X 699 GLU cc_start: 0.8074 (mp0) cc_final: 0.7711 (mp0) REVERT: X 704 ASP cc_start: 0.8500 (t70) cc_final: 0.8273 (t0) REVERT: X 707 LYS cc_start: 0.8872 (tptp) cc_final: 0.8309 (tptp) REVERT: X 718 ILE cc_start: 0.8858 (tp) cc_final: 0.8572 (tp) REVERT: X 768 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8383 (tm-30) REVERT: X 773 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8374 (tm-30) REVERT: Y 17 ASP cc_start: 0.8737 (p0) cc_final: 0.8510 (p0) REVERT: Y 42 GLN cc_start: 0.9013 (mp10) cc_final: 0.8601 (mp10) REVERT: Y 69 TYR cc_start: 0.6301 (m-80) cc_final: 0.5347 (m-80) REVERT: Y 107 LEU cc_start: 0.8682 (tp) cc_final: 0.8003 (tp) REVERT: Y 220 ILE cc_start: 0.7342 (tp) cc_final: 0.7005 (pt) REVERT: Y 273 ILE cc_start: 0.8685 (tp) cc_final: 0.8229 (pt) REVERT: Y 328 PHE cc_start: 0.8465 (t80) cc_final: 0.8219 (t80) REVERT: Y 380 CYS cc_start: 0.8459 (m) cc_final: 0.7787 (t) REVERT: Y 415 PHE cc_start: 0.7564 (t80) cc_final: 0.6971 (t80) REVERT: Y 500 GLU cc_start: 0.7341 (pt0) cc_final: 0.6227 (pp20) REVERT: Y 519 ASP cc_start: 0.7795 (m-30) cc_final: 0.7197 (m-30) REVERT: Y 527 MET cc_start: 0.8434 (ppp) cc_final: 0.8226 (ppp) REVERT: Y 539 ASP cc_start: 0.8046 (t70) cc_final: 0.7757 (t70) REVERT: Y 619 LEU cc_start: 0.8747 (mm) cc_final: 0.8336 (tp) REVERT: Y 634 ASP cc_start: 0.7718 (p0) cc_final: 0.7090 (p0) REVERT: Y 645 ILE cc_start: 0.8934 (pt) cc_final: 0.8724 (pt) REVERT: Y 662 GLU cc_start: 0.8941 (pt0) cc_final: 0.8375 (pt0) REVERT: Y 673 TYR cc_start: 0.8161 (m-80) cc_final: 0.7560 (m-80) REVERT: Y 680 ASP cc_start: 0.8000 (m-30) cc_final: 0.7719 (m-30) REVERT: Y 753 ARG cc_start: 0.7789 (ttt90) cc_final: 0.7551 (ttt90) REVERT: Y 769 GLN cc_start: 0.7372 (mm110) cc_final: 0.6962 (tp40) REVERT: Y 773 GLN cc_start: 0.8767 (tm-30) cc_final: 0.8231 (tm-30) REVERT: Z 1 MET cc_start: 0.8809 (tmm) cc_final: 0.8319 (tmm) REVERT: Z 5 ILE cc_start: 0.6452 (mm) cc_final: 0.6103 (mt) REVERT: Z 8 GLN cc_start: 0.7703 (pm20) cc_final: 0.7375 (pm20) REVERT: Z 271 ILE cc_start: 0.9432 (tp) cc_final: 0.8793 (tp) REVERT: Z 352 TYR cc_start: 0.7761 (m-80) cc_final: 0.7131 (m-80) REVERT: Z 356 TRP cc_start: 0.7184 (t-100) cc_final: 0.6708 (t-100) REVERT: Z 454 ASP cc_start: 0.9052 (t70) cc_final: 0.8733 (t0) REVERT: Z 505 PHE cc_start: 0.8564 (m-80) cc_final: 0.7952 (m-80) REVERT: Z 514 MET cc_start: 0.7523 (mtp) cc_final: 0.7055 (mtp) REVERT: Z 611 GLN cc_start: 0.8936 (mp10) cc_final: 0.8372 (mp10) REVERT: Z 623 GLU cc_start: 0.7402 (tp30) cc_final: 0.6774 (tp30) REVERT: Z 632 ASN cc_start: 0.8551 (t0) cc_final: 0.7628 (p0) REVERT: Z 659 ILE cc_start: 0.8870 (mm) cc_final: 0.8453 (tp) REVERT: Z 683 GLU cc_start: 0.7643 (pp20) cc_final: 0.6905 (pp20) REVERT: Z 689 LYS cc_start: 0.9134 (mmtm) cc_final: 0.8828 (mmmm) REVERT: Z 721 ILE cc_start: 0.9427 (mt) cc_final: 0.9126 (mp) REVERT: Z 728 LYS cc_start: 0.6187 (ttpt) cc_final: 0.5811 (tppt) REVERT: Z 748 ASP cc_start: 0.9013 (t0) cc_final: 0.8655 (t70) REVERT: Z 759 ASP cc_start: 0.8457 (p0) cc_final: 0.8060 (p0) REVERT: Z 764 ARG cc_start: 0.7828 (tpm170) cc_final: 0.7460 (tpm170) REVERT: Z 767 ILE cc_start: 0.9064 (tt) cc_final: 0.8664 (tt) outliers start: 3 outliers final: 1 residues processed: 513 average time/residue: 0.2997 time to fit residues: 225.6868 Evaluate side-chains 452 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 451 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 5.9990 chunk 179 optimal weight: 0.3980 chunk 39 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 199 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 8 GLN X 611 GLN X 757 ASN ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 731 ASN Z 739 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16581 Z= 0.213 Angle : 0.743 10.307 22523 Z= 0.379 Chirality : 0.047 0.315 2577 Planarity : 0.006 0.133 2917 Dihedral : 5.566 26.155 2239 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.09 % Favored : 88.76 % Rotamer: Outliers : 0.11 % Allowed : 2.18 % Favored : 97.71 % 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: -3.32 (0.17), residues: 2055 helix: -0.95 (0.21), residues: 553 sheet: -1.52 (0.23), residues: 490 loop : -3.38 (0.18), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 138 HIS 0.002 0.001 HIS Z 315 PHE 0.032 0.002 PHE Z 724 TYR 0.036 0.001 TYR X 673 ARG 0.008 0.001 ARG Z 618 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 510 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 29 LYS cc_start: 0.9071 (pptt) cc_final: 0.8731 (ptmm) REVERT: X 72 THR cc_start: 0.7933 (m) cc_final: 0.7726 (m) REVERT: X 81 TRP cc_start: 0.7222 (m100) cc_final: 0.5526 (m100) REVERT: X 140 PHE cc_start: 0.7165 (t80) cc_final: 0.6701 (t80) REVERT: X 141 ILE cc_start: 0.8504 (pt) cc_final: 0.8262 (pt) REVERT: X 142 ASP cc_start: 0.5511 (m-30) cc_final: 0.4554 (m-30) REVERT: X 168 MET cc_start: 0.7764 (pmm) cc_final: 0.7266 (pmm) REVERT: X 263 LYS cc_start: 0.8379 (tptt) cc_final: 0.8106 (ttmt) REVERT: X 356 TRP cc_start: 0.5623 (m-10) cc_final: 0.4651 (m-10) REVERT: X 371 LEU cc_start: 0.7599 (pt) cc_final: 0.7131 (pt) REVERT: X 423 SER cc_start: 0.9149 (t) cc_final: 0.8897 (p) REVERT: X 512 ILE cc_start: 0.9224 (mm) cc_final: 0.9005 (mm) REVERT: X 527 MET cc_start: 0.7446 (mtt) cc_final: 0.7077 (mtt) REVERT: X 530 MET cc_start: 0.8976 (ttt) cc_final: 0.8704 (tpp) REVERT: X 531 PHE cc_start: 0.9264 (m-10) cc_final: 0.8717 (m-10) REVERT: X 551 LYS cc_start: 0.9136 (ttmt) cc_final: 0.8729 (ttpt) REVERT: X 631 MET cc_start: 0.8782 (tpp) cc_final: 0.8275 (tpp) REVERT: X 635 ASP cc_start: 0.8830 (m-30) cc_final: 0.8408 (m-30) REVERT: X 645 ILE cc_start: 0.9218 (tp) cc_final: 0.8881 (pt) REVERT: X 665 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8597 (tm-30) REVERT: X 666 LYS cc_start: 0.9099 (mtmm) cc_final: 0.8477 (mtmm) REVERT: X 694 LYS cc_start: 0.8550 (tptp) cc_final: 0.8115 (tptt) REVERT: X 699 GLU cc_start: 0.8032 (mp0) cc_final: 0.7694 (mp0) REVERT: X 704 ASP cc_start: 0.8335 (t70) cc_final: 0.8072 (t0) REVERT: X 707 LYS cc_start: 0.8885 (tptp) cc_final: 0.8567 (tptp) REVERT: X 768 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8254 (tm-30) REVERT: X 769 GLN cc_start: 0.8509 (pp30) cc_final: 0.8266 (pp30) REVERT: Y 12 ASN cc_start: 0.7784 (m-40) cc_final: 0.7332 (p0) REVERT: Y 42 GLN cc_start: 0.8988 (mp10) cc_final: 0.8591 (mp10) REVERT: Y 107 LEU cc_start: 0.8668 (tp) cc_final: 0.8027 (tp) REVERT: Y 220 ILE cc_start: 0.7391 (tp) cc_final: 0.7098 (pt) REVERT: Y 263 LYS cc_start: 0.8485 (ttpp) cc_final: 0.7816 (ttpp) REVERT: Y 265 MET cc_start: 0.8821 (mmm) cc_final: 0.8598 (mmm) REVERT: Y 273 ILE cc_start: 0.8843 (tp) cc_final: 0.8155 (pt) REVERT: Y 275 PHE cc_start: 0.8062 (t80) cc_final: 0.7778 (t80) REVERT: Y 328 PHE cc_start: 0.8467 (t80) cc_final: 0.8243 (t80) REVERT: Y 337 PHE cc_start: 0.7945 (m-80) cc_final: 0.7666 (m-80) REVERT: Y 380 CYS cc_start: 0.8264 (m) cc_final: 0.7711 (t) REVERT: Y 415 PHE cc_start: 0.7589 (t80) cc_final: 0.6975 (t80) REVERT: Y 459 LYS cc_start: 0.6842 (ptpp) cc_final: 0.6622 (ptpp) REVERT: Y 471 ILE cc_start: 0.9467 (tp) cc_final: 0.9170 (tp) REVERT: Y 500 GLU cc_start: 0.6891 (pt0) cc_final: 0.6061 (pp20) REVERT: Y 519 ASP cc_start: 0.7665 (m-30) cc_final: 0.6799 (m-30) REVERT: Y 527 MET cc_start: 0.8474 (ppp) cc_final: 0.7728 (tmm) REVERT: Y 539 ASP cc_start: 0.8070 (t70) cc_final: 0.7786 (t70) REVERT: Y 619 LEU cc_start: 0.8734 (mm) cc_final: 0.8305 (tp) REVERT: Y 634 ASP cc_start: 0.7891 (p0) cc_final: 0.7265 (p0) REVERT: Y 662 GLU cc_start: 0.8936 (pt0) cc_final: 0.8368 (pt0) REVERT: Y 673 TYR cc_start: 0.8162 (m-80) cc_final: 0.7578 (m-80) REVERT: Y 680 ASP cc_start: 0.8005 (m-30) cc_final: 0.7750 (m-30) REVERT: Y 691 PHE cc_start: 0.8713 (m-80) cc_final: 0.7885 (m-80) REVERT: Y 753 ARG cc_start: 0.7780 (ttt90) cc_final: 0.7451 (ttt90) REVERT: Y 769 GLN cc_start: 0.7355 (mm110) cc_final: 0.6958 (tp40) REVERT: Y 773 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8239 (tm-30) REVERT: Z 1 MET cc_start: 0.8835 (tmm) cc_final: 0.8342 (tmm) REVERT: Z 5 ILE cc_start: 0.6182 (mm) cc_final: 0.5539 (mt) REVERT: Z 8 GLN cc_start: 0.7885 (pm20) cc_final: 0.7593 (pm20) REVERT: Z 271 ILE cc_start: 0.9387 (tp) cc_final: 0.8677 (tp) REVERT: Z 302 GLN cc_start: 0.8207 (pp30) cc_final: 0.7995 (pp30) REVERT: Z 356 TRP cc_start: 0.7233 (t-100) cc_final: 0.6580 (t-100) REVERT: Z 454 ASP cc_start: 0.9052 (t70) cc_final: 0.8711 (t0) REVERT: Z 494 LEU cc_start: 0.8436 (mp) cc_final: 0.8213 (tt) REVERT: Z 505 PHE cc_start: 0.8580 (m-80) cc_final: 0.7971 (m-80) REVERT: Z 514 MET cc_start: 0.7594 (mtp) cc_final: 0.7046 (mtp) REVERT: Z 528 PHE cc_start: 0.8615 (t80) cc_final: 0.8219 (t80) REVERT: Z 549 MET cc_start: 0.7770 (mmp) cc_final: 0.7370 (mmp) REVERT: Z 611 GLN cc_start: 0.8957 (mp10) cc_final: 0.8555 (mp10) REVERT: Z 623 GLU cc_start: 0.7546 (tp30) cc_final: 0.6990 (tp30) REVERT: Z 632 ASN cc_start: 0.8349 (t0) cc_final: 0.7582 (p0) REVERT: Z 659 ILE cc_start: 0.8800 (mm) cc_final: 0.8598 (mm) REVERT: Z 689 LYS cc_start: 0.9129 (mmtm) cc_final: 0.8873 (mmmm) REVERT: Z 718 ILE cc_start: 0.8997 (mp) cc_final: 0.8583 (mp) REVERT: Z 721 ILE cc_start: 0.9365 (mt) cc_final: 0.8740 (mt) REVERT: Z 728 LYS cc_start: 0.6204 (ttpt) cc_final: 0.5828 (tppt) REVERT: Z 739 GLN cc_start: 0.8053 (tp40) cc_final: 0.7721 (tp40) REVERT: Z 748 ASP cc_start: 0.9021 (t0) cc_final: 0.8665 (t70) REVERT: Z 754 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8408 (tm-30) REVERT: Z 759 ASP cc_start: 0.8430 (p0) cc_final: 0.8099 (p0) REVERT: Z 764 ARG cc_start: 0.7687 (tpm170) cc_final: 0.7268 (tpm170) REVERT: Z 767 ILE cc_start: 0.9074 (tt) cc_final: 0.8673 (tt) outliers start: 2 outliers final: 0 residues processed: 511 average time/residue: 0.2952 time to fit residues: 220.5295 Evaluate side-chains 453 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 1.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 112 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 422 ASN X 757 ASN ** Y 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 731 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16581 Z= 0.293 Angle : 0.773 9.809 22523 Z= 0.399 Chirality : 0.048 0.241 2577 Planarity : 0.006 0.111 2917 Dihedral : 5.716 25.398 2239 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.73 % Favored : 88.13 % Rotamer: Outliers : 0.11 % Allowed : 2.34 % Favored : 97.55 % 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: -3.36 (0.17), residues: 2055 helix: -1.03 (0.21), residues: 556 sheet: -1.61 (0.23), residues: 494 loop : -3.35 (0.18), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP X 356 HIS 0.003 0.001 HIS X 188 PHE 0.035 0.002 PHE X 724 TYR 0.025 0.002 TYR Z 461 ARG 0.014 0.001 ARG Y 750 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 501 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 8 GLN cc_start: 0.8617 (pt0) cc_final: 0.7832 (pp30) REVERT: X 20 ASP cc_start: 0.8855 (p0) cc_final: 0.8652 (p0) REVERT: X 25 ILE cc_start: 0.8670 (tp) cc_final: 0.8361 (tp) REVERT: X 140 PHE cc_start: 0.7279 (t80) cc_final: 0.6926 (t80) REVERT: X 423 SER cc_start: 0.9180 (t) cc_final: 0.8941 (p) REVERT: X 512 ILE cc_start: 0.9244 (mm) cc_final: 0.9026 (mm) REVERT: X 530 MET cc_start: 0.8997 (ttt) cc_final: 0.8752 (tpp) REVERT: X 551 LYS cc_start: 0.9142 (ttmt) cc_final: 0.8720 (ttpt) REVERT: X 635 ASP cc_start: 0.8832 (m-30) cc_final: 0.8600 (m-30) REVERT: X 645 ILE cc_start: 0.9255 (tp) cc_final: 0.8896 (pt) REVERT: X 662 GLU cc_start: 0.8125 (pm20) cc_final: 0.7833 (pm20) REVERT: X 665 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8611 (tm-30) REVERT: X 694 LYS cc_start: 0.8609 (tptp) cc_final: 0.8104 (tptt) REVERT: X 699 GLU cc_start: 0.8130 (mp0) cc_final: 0.7804 (mp0) REVERT: X 704 ASP cc_start: 0.8402 (t70) cc_final: 0.8084 (t0) REVERT: X 707 LYS cc_start: 0.8955 (tptp) cc_final: 0.8695 (tptp) REVERT: X 718 ILE cc_start: 0.9089 (tp) cc_final: 0.8504 (tp) REVERT: Y 4 LEU cc_start: 0.7091 (pt) cc_final: 0.6316 (pt) REVERT: Y 8 GLN cc_start: 0.8329 (mp10) cc_final: 0.7592 (mp10) REVERT: Y 9 LEU cc_start: 0.8840 (mt) cc_final: 0.8627 (mt) REVERT: Y 12 ASN cc_start: 0.7683 (m-40) cc_final: 0.7381 (m-40) REVERT: Y 17 ASP cc_start: 0.8779 (p0) cc_final: 0.8366 (p0) REVERT: Y 24 GLU cc_start: 0.9367 (tm-30) cc_final: 0.9153 (tm-30) REVERT: Y 106 ILE cc_start: 0.8521 (tp) cc_final: 0.8183 (tp) REVERT: Y 107 LEU cc_start: 0.8646 (tp) cc_final: 0.8371 (tp) REVERT: Y 220 ILE cc_start: 0.7527 (tp) cc_final: 0.7245 (pt) REVERT: Y 273 ILE cc_start: 0.8954 (tp) cc_final: 0.8541 (tp) REVERT: Y 275 PHE cc_start: 0.8233 (t80) cc_final: 0.7941 (t80) REVERT: Y 328 PHE cc_start: 0.8420 (t80) cc_final: 0.8184 (t80) REVERT: Y 337 PHE cc_start: 0.7957 (m-80) cc_final: 0.7549 (m-80) REVERT: Y 342 PHE cc_start: 0.7538 (t80) cc_final: 0.7323 (t80) REVERT: Y 352 TYR cc_start: 0.8699 (m-80) cc_final: 0.8393 (m-10) REVERT: Y 380 CYS cc_start: 0.8211 (m) cc_final: 0.7704 (t) REVERT: Y 415 PHE cc_start: 0.7569 (t80) cc_final: 0.7052 (t80) REVERT: Y 471 ILE cc_start: 0.9483 (tp) cc_final: 0.9205 (tp) REVERT: Y 519 ASP cc_start: 0.7781 (m-30) cc_final: 0.7441 (m-30) REVERT: Y 522 LEU cc_start: 0.9283 (tp) cc_final: 0.9075 (tp) REVERT: Y 527 MET cc_start: 0.8595 (ppp) cc_final: 0.8270 (ppp) REVERT: Y 539 ASP cc_start: 0.8130 (t70) cc_final: 0.7885 (t70) REVERT: Y 547 ASN cc_start: 0.8856 (m110) cc_final: 0.8655 (m-40) REVERT: Y 549 MET cc_start: 0.8225 (mtm) cc_final: 0.7466 (mmm) REVERT: Y 619 LEU cc_start: 0.8809 (mm) cc_final: 0.8069 (tp) REVERT: Y 634 ASP cc_start: 0.7795 (p0) cc_final: 0.7212 (p0) REVERT: Y 662 GLU cc_start: 0.8966 (pt0) cc_final: 0.8373 (pt0) REVERT: Y 673 TYR cc_start: 0.8259 (m-80) cc_final: 0.7728 (m-10) REVERT: Y 691 PHE cc_start: 0.8834 (m-80) cc_final: 0.7832 (m-80) REVERT: Y 769 GLN cc_start: 0.6899 (mm110) cc_final: 0.6464 (tp40) REVERT: Y 773 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8255 (tm-30) REVERT: Z 5 ILE cc_start: 0.6309 (mm) cc_final: 0.5805 (mt) REVERT: Z 8 GLN cc_start: 0.7765 (pm20) cc_final: 0.7301 (pm20) REVERT: Z 21 GLU cc_start: 0.8487 (tt0) cc_final: 0.7646 (tm-30) REVERT: Z 271 ILE cc_start: 0.9347 (tp) cc_final: 0.8815 (tp) REVERT: Z 273 ILE cc_start: 0.9043 (tp) cc_final: 0.8781 (tp) REVERT: Z 276 LYS cc_start: 0.9044 (tptm) cc_final: 0.8431 (ttmm) REVERT: Z 302 GLN cc_start: 0.8322 (pp30) cc_final: 0.8062 (pp30) REVERT: Z 371 LEU cc_start: 0.9249 (tp) cc_final: 0.8903 (tp) REVERT: Z 497 GLN cc_start: 0.8476 (pm20) cc_final: 0.8021 (pm20) REVERT: Z 505 PHE cc_start: 0.8660 (m-80) cc_final: 0.7951 (m-80) REVERT: Z 528 PHE cc_start: 0.8661 (t80) cc_final: 0.8335 (t80) REVERT: Z 549 MET cc_start: 0.7699 (mmp) cc_final: 0.7452 (mmp) REVERT: Z 611 GLN cc_start: 0.9007 (mp10) cc_final: 0.8603 (mp10) REVERT: Z 623 GLU cc_start: 0.7626 (tp30) cc_final: 0.6906 (tp30) REVERT: Z 632 ASN cc_start: 0.8447 (t0) cc_final: 0.7847 (p0) REVERT: Z 659 ILE cc_start: 0.8895 (mm) cc_final: 0.8529 (tp) REVERT: Z 674 ARG cc_start: 0.8960 (ptp-110) cc_final: 0.8489 (ptp90) REVERT: Z 689 LYS cc_start: 0.9256 (mmtm) cc_final: 0.9035 (mmmm) REVERT: Z 721 ILE cc_start: 0.9391 (mt) cc_final: 0.9053 (mp) REVERT: Z 728 LYS cc_start: 0.6251 (ttpt) cc_final: 0.5847 (tppt) REVERT: Z 748 ASP cc_start: 0.9022 (t0) cc_final: 0.8741 (t0) REVERT: Z 759 ASP cc_start: 0.8473 (p0) cc_final: 0.8176 (p0) REVERT: Z 764 ARG cc_start: 0.7870 (tpm170) cc_final: 0.7256 (tpm170) REVERT: Z 767 ILE cc_start: 0.9030 (tt) cc_final: 0.8633 (tt) outliers start: 2 outliers final: 0 residues processed: 502 average time/residue: 0.3221 time to fit residues: 239.8845 Evaluate side-chains 442 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 442 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 118 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 chunk 126 optimal weight: 0.0970 chunk 135 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 156 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 221 ASN X 757 ASN Y 266 GLN ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 731 ASN Z 324 ASN Z 348 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16581 Z= 0.214 Angle : 0.773 11.461 22523 Z= 0.392 Chirality : 0.049 0.320 2577 Planarity : 0.006 0.069 2917 Dihedral : 5.621 25.411 2239 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.46 % Favored : 89.39 % Rotamer: Outliers : 0.11 % Allowed : 1.31 % Favored : 98.58 % 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: -3.25 (0.17), residues: 2055 helix: -1.01 (0.21), residues: 547 sheet: -1.42 (0.23), residues: 493 loop : -3.28 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP X 356 HIS 0.002 0.000 HIS X 188 PHE 0.037 0.002 PHE X 505 TYR 0.037 0.002 TYR X 461 ARG 0.010 0.001 ARG Y 620 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 506 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 8 GLN cc_start: 0.8455 (pt0) cc_final: 0.7700 (pp30) REVERT: X 21 GLU cc_start: 0.8521 (pp20) cc_final: 0.8154 (tm-30) REVERT: X 25 ILE cc_start: 0.8670 (tp) cc_final: 0.8275 (tp) REVERT: X 81 TRP cc_start: 0.7385 (m100) cc_final: 0.5664 (m100) REVERT: X 140 PHE cc_start: 0.7073 (t80) cc_final: 0.6707 (t80) REVERT: X 141 ILE cc_start: 0.8512 (pt) cc_final: 0.8245 (pt) REVERT: X 142 ASP cc_start: 0.5451 (m-30) cc_final: 0.4549 (m-30) REVERT: X 168 MET cc_start: 0.8035 (pmm) cc_final: 0.7492 (pmm) REVERT: X 356 TRP cc_start: 0.5424 (m-10) cc_final: 0.4703 (m-10) REVERT: X 371 LEU cc_start: 0.7626 (pt) cc_final: 0.7174 (pt) REVERT: X 375 LEU cc_start: 0.8879 (mm) cc_final: 0.8579 (mt) REVERT: X 423 SER cc_start: 0.9030 (t) cc_final: 0.8821 (p) REVERT: X 512 ILE cc_start: 0.9235 (mm) cc_final: 0.8987 (mm) REVERT: X 551 LYS cc_start: 0.9152 (ttmt) cc_final: 0.8729 (ttpt) REVERT: X 635 ASP cc_start: 0.8783 (m-30) cc_final: 0.8006 (m-30) REVERT: X 645 ILE cc_start: 0.9233 (tp) cc_final: 0.8854 (pt) REVERT: X 665 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8589 (tm-30) REVERT: X 694 LYS cc_start: 0.8629 (tptp) cc_final: 0.8154 (tptt) REVERT: X 699 GLU cc_start: 0.8097 (mp0) cc_final: 0.7776 (mp0) REVERT: X 704 ASP cc_start: 0.8393 (t70) cc_final: 0.8113 (t0) REVERT: X 718 ILE cc_start: 0.9029 (tp) cc_final: 0.8567 (tp) REVERT: Y 4 LEU cc_start: 0.7168 (pt) cc_final: 0.6495 (pt) REVERT: Y 8 GLN cc_start: 0.8399 (mp10) cc_final: 0.8051 (mp10) REVERT: Y 12 ASN cc_start: 0.7789 (m-40) cc_final: 0.7342 (p0) REVERT: Y 17 ASP cc_start: 0.8754 (p0) cc_final: 0.8322 (p0) REVERT: Y 106 ILE cc_start: 0.8422 (tp) cc_final: 0.8073 (tp) REVERT: Y 107 LEU cc_start: 0.8599 (tp) cc_final: 0.8329 (tp) REVERT: Y 175 TYR cc_start: 0.6773 (m-80) cc_final: 0.6362 (m-80) REVERT: Y 220 ILE cc_start: 0.7659 (tp) cc_final: 0.7362 (pt) REVERT: Y 263 LYS cc_start: 0.8378 (ttpp) cc_final: 0.7738 (ttpp) REVERT: Y 273 ILE cc_start: 0.8927 (tp) cc_final: 0.8393 (tp) REVERT: Y 328 PHE cc_start: 0.8456 (t80) cc_final: 0.8241 (t80) REVERT: Y 337 PHE cc_start: 0.7929 (m-80) cc_final: 0.7727 (m-80) REVERT: Y 342 PHE cc_start: 0.7406 (t80) cc_final: 0.7135 (t80) REVERT: Y 380 CYS cc_start: 0.8245 (m) cc_final: 0.7624 (t) REVERT: Y 415 PHE cc_start: 0.7557 (t80) cc_final: 0.6995 (t80) REVERT: Y 471 ILE cc_start: 0.9459 (tp) cc_final: 0.9202 (tp) REVERT: Y 500 GLU cc_start: 0.7542 (pt0) cc_final: 0.6464 (pp20) REVERT: Y 501 LEU cc_start: 0.9294 (tp) cc_final: 0.8971 (tp) REVERT: Y 519 ASP cc_start: 0.7801 (m-30) cc_final: 0.7112 (m-30) REVERT: Y 527 MET cc_start: 0.8532 (ppp) cc_final: 0.8204 (ppp) REVERT: Y 539 ASP cc_start: 0.8083 (t70) cc_final: 0.7832 (t70) REVERT: Y 619 LEU cc_start: 0.8644 (mm) cc_final: 0.8059 (tp) REVERT: Y 662 GLU cc_start: 0.8965 (pt0) cc_final: 0.8358 (pt0) REVERT: Y 673 TYR cc_start: 0.8131 (m-80) cc_final: 0.7798 (m-80) REVERT: Y 691 PHE cc_start: 0.8684 (m-80) cc_final: 0.7863 (m-80) REVERT: Y 724 PHE cc_start: 0.6935 (m-80) cc_final: 0.6025 (m-80) REVERT: Y 732 ASP cc_start: 0.7051 (t0) cc_final: 0.6706 (t0) REVERT: Y 743 ASN cc_start: 0.8874 (m-40) cc_final: 0.8546 (m-40) REVERT: Y 753 ARG cc_start: 0.7895 (ttt90) cc_final: 0.7650 (ttt90) REVERT: Y 769 GLN cc_start: 0.7156 (mm110) cc_final: 0.6753 (tp40) REVERT: Y 773 GLN cc_start: 0.8730 (tm-30) cc_final: 0.8227 (tm-30) REVERT: Z 5 ILE cc_start: 0.5875 (mm) cc_final: 0.5416 (mt) REVERT: Z 8 GLN cc_start: 0.7501 (pm20) cc_final: 0.7268 (pm20) REVERT: Z 21 GLU cc_start: 0.8510 (tt0) cc_final: 0.7772 (tm-30) REVERT: Z 271 ILE cc_start: 0.9398 (tp) cc_final: 0.8815 (tp) REVERT: Z 273 ILE cc_start: 0.8972 (tp) cc_final: 0.8751 (tp) REVERT: Z 302 GLN cc_start: 0.8342 (pp30) cc_final: 0.8030 (pp30) REVERT: Z 352 TYR cc_start: 0.7544 (m-80) cc_final: 0.7234 (m-10) REVERT: Z 357 ASP cc_start: 0.7991 (m-30) cc_final: 0.7163 (m-30) REVERT: Z 371 LEU cc_start: 0.9203 (tp) cc_final: 0.8827 (tp) REVERT: Z 497 GLN cc_start: 0.8484 (pm20) cc_final: 0.8137 (pm20) REVERT: Z 505 PHE cc_start: 0.8445 (m-80) cc_final: 0.7731 (m-80) REVERT: Z 514 MET cc_start: 0.7650 (mtp) cc_final: 0.7179 (mtp) REVERT: Z 528 PHE cc_start: 0.8540 (t80) cc_final: 0.8081 (t80) REVERT: Z 611 GLN cc_start: 0.8942 (mp10) cc_final: 0.8496 (mp10) REVERT: Z 623 GLU cc_start: 0.7550 (tp30) cc_final: 0.6892 (mm-30) REVERT: Z 632 ASN cc_start: 0.8363 (t0) cc_final: 0.7766 (p0) REVERT: Z 659 ILE cc_start: 0.8885 (mm) cc_final: 0.8522 (tp) REVERT: Z 674 ARG cc_start: 0.9018 (ptp-110) cc_final: 0.8584 (ptp90) REVERT: Z 689 LYS cc_start: 0.9131 (mmtm) cc_final: 0.8898 (mmmm) REVERT: Z 721 ILE cc_start: 0.9379 (mt) cc_final: 0.8743 (mt) REVERT: Z 728 LYS cc_start: 0.6222 (ttpt) cc_final: 0.6002 (tppt) REVERT: Z 739 GLN cc_start: 0.8242 (tp40) cc_final: 0.7906 (tp40) REVERT: Z 748 ASP cc_start: 0.9129 (t0) cc_final: 0.8765 (t0) REVERT: Z 750 ARG cc_start: 0.8570 (tpp80) cc_final: 0.8266 (tpp80) REVERT: Z 759 ASP cc_start: 0.8414 (p0) cc_final: 0.8126 (p0) REVERT: Z 764 ARG cc_start: 0.7810 (tpm170) cc_final: 0.7124 (tpm170) REVERT: Z 767 ILE cc_start: 0.9045 (tt) cc_final: 0.8632 (tt) outliers start: 2 outliers final: 1 residues processed: 507 average time/residue: 0.2954 time to fit residues: 218.1165 Evaluate side-chains 443 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 173 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 0.4980 chunk 145 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 221 ASN ** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 731 ASN ** Z 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 16581 Z= 0.280 Angle : 0.787 11.179 22523 Z= 0.402 Chirality : 0.049 0.450 2577 Planarity : 0.006 0.070 2917 Dihedral : 5.701 25.788 2239 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.58 % Favored : 88.27 % Rotamer: Outliers : 0.05 % Allowed : 1.03 % Favored : 98.91 % 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: -3.29 (0.18), residues: 2055 helix: -1.01 (0.21), residues: 552 sheet: -1.60 (0.22), residues: 513 loop : -3.27 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP X 356 HIS 0.003 0.001 HIS Z 315 PHE 0.043 0.002 PHE X 505 TYR 0.025 0.002 TYR Z 461 ARG 0.009 0.001 ARG Y 750 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 494 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 21 GLU cc_start: 0.8539 (pp20) cc_final: 0.8250 (tm-30) REVERT: X 25 ILE cc_start: 0.8653 (tp) cc_final: 0.8207 (tp) REVERT: X 140 PHE cc_start: 0.7155 (t80) cc_final: 0.6751 (t80) REVERT: X 141 ILE cc_start: 0.8529 (pt) cc_final: 0.8260 (pt) REVERT: X 142 ASP cc_start: 0.5633 (m-30) cc_final: 0.4593 (m-30) REVERT: X 265 MET cc_start: 0.8722 (mmm) cc_final: 0.8404 (mmm) REVERT: X 356 TRP cc_start: 0.5897 (m-10) cc_final: 0.5506 (m-10) REVERT: X 371 LEU cc_start: 0.7645 (pt) cc_final: 0.7270 (pt) REVERT: X 423 SER cc_start: 0.9030 (t) cc_final: 0.8793 (p) REVERT: X 512 ILE cc_start: 0.9213 (mm) cc_final: 0.8919 (mm) REVERT: X 530 MET cc_start: 0.9015 (tpp) cc_final: 0.8811 (tpp) REVERT: X 551 LYS cc_start: 0.9162 (ttmt) cc_final: 0.8727 (ttpt) REVERT: X 631 MET cc_start: 0.8799 (tpp) cc_final: 0.8354 (tpp) REVERT: X 635 ASP cc_start: 0.8764 (m-30) cc_final: 0.8348 (m-30) REVERT: X 662 GLU cc_start: 0.8276 (pm20) cc_final: 0.8013 (pm20) REVERT: X 665 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8647 (tm-30) REVERT: X 673 TYR cc_start: 0.8717 (m-80) cc_final: 0.8381 (m-80) REVERT: X 694 LYS cc_start: 0.8600 (tptp) cc_final: 0.8121 (tptt) REVERT: X 699 GLU cc_start: 0.8143 (mp0) cc_final: 0.7780 (mp0) REVERT: X 704 ASP cc_start: 0.8399 (t70) cc_final: 0.8099 (t0) REVERT: X 707 LYS cc_start: 0.8941 (tptp) cc_final: 0.8537 (tptp) REVERT: X 768 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8226 (tm-30) REVERT: Y 4 LEU cc_start: 0.7150 (pt) cc_final: 0.6360 (pt) REVERT: Y 8 GLN cc_start: 0.8441 (mp10) cc_final: 0.7688 (mp10) REVERT: Y 9 LEU cc_start: 0.8877 (mt) cc_final: 0.8624 (mt) REVERT: Y 17 ASP cc_start: 0.8840 (p0) cc_final: 0.8477 (p0) REVERT: Y 24 GLU cc_start: 0.9352 (tm-30) cc_final: 0.9092 (tm-30) REVERT: Y 106 ILE cc_start: 0.8504 (tp) cc_final: 0.8113 (tp) REVERT: Y 107 LEU cc_start: 0.8685 (tp) cc_final: 0.8430 (tp) REVERT: Y 220 ILE cc_start: 0.7686 (tp) cc_final: 0.7480 (pt) REVERT: Y 253 ASP cc_start: 0.9040 (p0) cc_final: 0.8783 (p0) REVERT: Y 328 PHE cc_start: 0.8457 (t80) cc_final: 0.8254 (t80) REVERT: Y 337 PHE cc_start: 0.7980 (m-80) cc_final: 0.7765 (m-80) REVERT: Y 342 PHE cc_start: 0.7485 (t80) cc_final: 0.7238 (t80) REVERT: Y 380 CYS cc_start: 0.8192 (m) cc_final: 0.7670 (t) REVERT: Y 415 PHE cc_start: 0.7670 (t80) cc_final: 0.7137 (t80) REVERT: Y 471 ILE cc_start: 0.9463 (tp) cc_final: 0.9184 (tp) REVERT: Y 500 GLU cc_start: 0.7358 (pt0) cc_final: 0.6235 (pp20) REVERT: Y 501 LEU cc_start: 0.9344 (tp) cc_final: 0.8982 (tp) REVERT: Y 519 ASP cc_start: 0.7722 (m-30) cc_final: 0.6948 (m-30) REVERT: Y 527 MET cc_start: 0.8579 (ppp) cc_final: 0.8194 (ppp) REVERT: Y 539 ASP cc_start: 0.8127 (t70) cc_final: 0.7906 (t70) REVERT: Y 549 MET cc_start: 0.8158 (mtm) cc_final: 0.7532 (tmm) REVERT: Y 634 ASP cc_start: 0.8019 (p0) cc_final: 0.7265 (p0) REVERT: Y 662 GLU cc_start: 0.9009 (pt0) cc_final: 0.8427 (pt0) REVERT: Y 673 TYR cc_start: 0.8246 (m-80) cc_final: 0.7928 (m-80) REVERT: Y 691 PHE cc_start: 0.8786 (m-80) cc_final: 0.7869 (m-80) REVERT: Y 724 PHE cc_start: 0.7117 (m-10) cc_final: 0.5759 (m-80) REVERT: Y 743 ASN cc_start: 0.8977 (m-40) cc_final: 0.8636 (m-40) REVERT: Y 753 ARG cc_start: 0.7973 (ttt90) cc_final: 0.7745 (ttt90) REVERT: Y 769 GLN cc_start: 0.6963 (mm110) cc_final: 0.6457 (tp40) REVERT: Y 773 GLN cc_start: 0.8744 (tm-30) cc_final: 0.8208 (tm-30) REVERT: Z 1 MET cc_start: 0.8894 (tmm) cc_final: 0.8641 (tmm) REVERT: Z 5 ILE cc_start: 0.5598 (mm) cc_final: 0.5148 (mt) REVERT: Z 8 GLN cc_start: 0.7888 (pm20) cc_final: 0.7499 (pm20) REVERT: Z 21 GLU cc_start: 0.8518 (tt0) cc_final: 0.8010 (tm-30) REVERT: Z 271 ILE cc_start: 0.9387 (tp) cc_final: 0.8826 (tp) REVERT: Z 357 ASP cc_start: 0.8256 (m-30) cc_final: 0.7319 (m-30) REVERT: Z 371 LEU cc_start: 0.9240 (tp) cc_final: 0.8895 (tp) REVERT: Z 454 ASP cc_start: 0.9058 (t70) cc_final: 0.8748 (t0) REVERT: Z 497 GLN cc_start: 0.8664 (pm20) cc_final: 0.8240 (pm20) REVERT: Z 528 PHE cc_start: 0.8540 (t80) cc_final: 0.8086 (t80) REVERT: Z 611 GLN cc_start: 0.9010 (mp10) cc_final: 0.8594 (mp10) REVERT: Z 623 GLU cc_start: 0.7647 (tp30) cc_final: 0.7039 (mm-30) REVERT: Z 632 ASN cc_start: 0.8430 (t0) cc_final: 0.7823 (p0) REVERT: Z 659 ILE cc_start: 0.8903 (mm) cc_final: 0.8543 (tp) REVERT: Z 674 ARG cc_start: 0.9025 (ptp-110) cc_final: 0.8560 (ptp90) REVERT: Z 689 LYS cc_start: 0.9261 (mmtm) cc_final: 0.9057 (mmmm) REVERT: Z 721 ILE cc_start: 0.9442 (mt) cc_final: 0.9091 (mp) REVERT: Z 728 LYS cc_start: 0.6292 (ttpt) cc_final: 0.6011 (tppt) REVERT: Z 748 ASP cc_start: 0.9177 (t0) cc_final: 0.8797 (t70) REVERT: Z 754 GLU cc_start: 0.8437 (pt0) cc_final: 0.8158 (pt0) REVERT: Z 759 ASP cc_start: 0.8478 (p0) cc_final: 0.8202 (p0) outliers start: 1 outliers final: 0 residues processed: 494 average time/residue: 0.2910 time to fit residues: 210.5958 Evaluate side-chains 430 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 430 time to evaluate : 1.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 6.9990 chunk 195 optimal weight: 0.9980 chunk 119 optimal weight: 0.2980 chunk 92 optimal weight: 0.5980 chunk 136 optimal weight: 0.0980 chunk 205 optimal weight: 5.9990 chunk 188 optimal weight: 0.0870 chunk 163 optimal weight: 6.9990 chunk 16 optimal weight: 8.9990 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 8 GLN X 221 ASN ** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 731 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16581 Z= 0.211 Angle : 0.792 16.604 22523 Z= 0.399 Chirality : 0.049 0.419 2577 Planarity : 0.005 0.063 2917 Dihedral : 5.538 25.173 2239 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.07 % Favored : 89.78 % Rotamer: Outliers : 0.05 % Allowed : 0.33 % Favored : 99.62 % 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: -3.23 (0.18), residues: 2055 helix: -0.98 (0.21), residues: 554 sheet: -1.36 (0.23), residues: 498 loop : -3.32 (0.18), residues: 1003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP X 356 HIS 0.002 0.001 HIS X 315 PHE 0.061 0.002 PHE X 505 TYR 0.031 0.002 TYR Z 305 ARG 0.009 0.001 ARG Y 750 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4110 Ramachandran restraints generated. 2055 Oldfield, 0 Emsley, 2055 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 487 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 21 GLU cc_start: 0.8479 (pp20) cc_final: 0.8246 (tm-30) REVERT: X 24 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8669 (tm-30) REVERT: X 25 ILE cc_start: 0.8520 (tp) cc_final: 0.8099 (tp) REVERT: X 81 TRP cc_start: 0.7326 (m100) cc_final: 0.5503 (m100) REVERT: X 140 PHE cc_start: 0.6931 (t80) cc_final: 0.6690 (t80) REVERT: X 141 ILE cc_start: 0.8477 (pt) cc_final: 0.8222 (pt) REVERT: X 142 ASP cc_start: 0.5408 (m-30) cc_final: 0.4482 (m-30) REVERT: X 168 MET cc_start: 0.7804 (pmm) cc_final: 0.7199 (pmm) REVERT: X 371 LEU cc_start: 0.7594 (pt) cc_final: 0.7093 (pt) REVERT: X 375 LEU cc_start: 0.8884 (mm) cc_final: 0.8592 (mt) REVERT: X 423 SER cc_start: 0.9113 (t) cc_final: 0.8897 (p) REVERT: X 508 LEU cc_start: 0.9378 (pp) cc_final: 0.9168 (pp) REVERT: X 530 MET cc_start: 0.9026 (tpp) cc_final: 0.8815 (tpp) REVERT: X 551 LYS cc_start: 0.9139 (ttmt) cc_final: 0.8853 (ttmt) REVERT: X 631 MET cc_start: 0.8481 (tpp) cc_final: 0.8042 (tpp) REVERT: X 635 ASP cc_start: 0.8792 (m-30) cc_final: 0.8513 (m-30) REVERT: X 658 ASP cc_start: 0.8071 (p0) cc_final: 0.7817 (p0) REVERT: X 665 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8659 (tm-30) REVERT: X 673 TYR cc_start: 0.8621 (m-80) cc_final: 0.8239 (m-80) REVERT: X 694 LYS cc_start: 0.8698 (tptp) cc_final: 0.8246 (tptt) REVERT: X 699 GLU cc_start: 0.8001 (mp0) cc_final: 0.7726 (mp0) REVERT: X 704 ASP cc_start: 0.8356 (t70) cc_final: 0.8059 (t0) REVERT: X 707 LYS cc_start: 0.8903 (tptp) cc_final: 0.8492 (tptp) REVERT: X 718 ILE cc_start: 0.8919 (tp) cc_final: 0.8707 (tp) REVERT: X 725 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8579 (mmmt) REVERT: Y 4 LEU cc_start: 0.7122 (pt) cc_final: 0.6392 (pt) REVERT: Y 8 GLN cc_start: 0.8515 (mp10) cc_final: 0.8226 (mp10) REVERT: Y 12 ASN cc_start: 0.7917 (m-40) cc_final: 0.7656 (p0) REVERT: Y 17 ASP cc_start: 0.8786 (p0) cc_final: 0.8432 (p0) REVERT: Y 175 TYR cc_start: 0.7336 (m-80) cc_final: 0.6431 (m-10) REVERT: Y 220 ILE cc_start: 0.7762 (tp) cc_final: 0.7497 (pt) REVERT: Y 273 ILE cc_start: 0.8709 (tp) cc_final: 0.8135 (tp) REVERT: Y 328 PHE cc_start: 0.8535 (t80) cc_final: 0.8319 (t80) REVERT: Y 342 PHE cc_start: 0.7340 (t80) cc_final: 0.7101 (t80) REVERT: Y 380 CYS cc_start: 0.8353 (m) cc_final: 0.7646 (t) REVERT: Y 415 PHE cc_start: 0.7548 (t80) cc_final: 0.7011 (t80) REVERT: Y 500 GLU cc_start: 0.7356 (pt0) cc_final: 0.6324 (pp20) REVERT: Y 519 ASP cc_start: 0.7729 (m-30) cc_final: 0.6573 (m-30) REVERT: Y 527 MET cc_start: 0.8549 (ppp) cc_final: 0.8142 (ppp) REVERT: Y 634 ASP cc_start: 0.7896 (p0) cc_final: 0.7237 (p0) REVERT: Y 662 GLU cc_start: 0.8985 (pt0) cc_final: 0.8415 (pt0) REVERT: Y 673 TYR cc_start: 0.8110 (m-80) cc_final: 0.7905 (m-80) REVERT: Y 691 PHE cc_start: 0.8746 (m-80) cc_final: 0.7915 (m-80) REVERT: Y 724 PHE cc_start: 0.6680 (m-10) cc_final: 0.5656 (m-80) REVERT: Y 732 ASP cc_start: 0.7017 (t0) cc_final: 0.6680 (t0) REVERT: Y 743 ASN cc_start: 0.8880 (m-40) cc_final: 0.8511 (m-40) REVERT: Y 753 ARG cc_start: 0.7887 (ttt90) cc_final: 0.7597 (ttt90) REVERT: Y 769 GLN cc_start: 0.7234 (mm110) cc_final: 0.6892 (tp40) REVERT: Y 773 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8109 (tm-30) REVERT: Z 1 MET cc_start: 0.8820 (tmm) cc_final: 0.8616 (tmm) REVERT: Z 5 ILE cc_start: 0.5754 (mm) cc_final: 0.5291 (mt) REVERT: Z 8 GLN cc_start: 0.7548 (pm20) cc_final: 0.7224 (pm20) REVERT: Z 21 GLU cc_start: 0.8495 (tt0) cc_final: 0.8026 (tm-30) REVERT: Z 271 ILE cc_start: 0.9187 (tp) cc_final: 0.8644 (tp) REVERT: Z 352 TYR cc_start: 0.7476 (m-80) cc_final: 0.7210 (m-10) REVERT: Z 357 ASP cc_start: 0.8032 (m-30) cc_final: 0.6996 (m-30) REVERT: Z 371 LEU cc_start: 0.9202 (tp) cc_final: 0.8838 (tp) REVERT: Z 497 GLN cc_start: 0.8516 (pm20) cc_final: 0.8063 (pm20) REVERT: Z 505 PHE cc_start: 0.8421 (m-80) cc_final: 0.7712 (m-80) REVERT: Z 514 MET cc_start: 0.6867 (mtp) cc_final: 0.6542 (mtp) REVERT: Z 528 PHE cc_start: 0.8430 (t80) cc_final: 0.7905 (t80) REVERT: Z 623 GLU cc_start: 0.7552 (tp30) cc_final: 0.6930 (mm-30) REVERT: Z 632 ASN cc_start: 0.8333 (t0) cc_final: 0.7621 (p0) REVERT: Z 659 ILE cc_start: 0.8868 (mm) cc_final: 0.8519 (tp) REVERT: Z 674 ARG cc_start: 0.8913 (ptp-110) cc_final: 0.8545 (ptp90) REVERT: Z 706 GLN cc_start: 0.8093 (pm20) cc_final: 0.7832 (pm20) REVERT: Z 721 ILE cc_start: 0.9445 (mt) cc_final: 0.9184 (mp) REVERT: Z 728 LYS cc_start: 0.6245 (ttpt) cc_final: 0.5903 (tppt) REVERT: Z 739 GLN cc_start: 0.8206 (tp40) cc_final: 0.7830 (tp40) REVERT: Z 748 ASP cc_start: 0.9224 (t0) cc_final: 0.8922 (t70) REVERT: Z 755 PHE cc_start: 0.9003 (t80) cc_final: 0.8423 (t80) REVERT: Z 759 ASP cc_start: 0.8414 (p0) cc_final: 0.8150 (p0) REVERT: Z 763 ILE cc_start: 0.9297 (pt) cc_final: 0.8854 (pt) outliers start: 1 outliers final: 0 residues processed: 487 average time/residue: 0.2965 time to fit residues: 213.8173 Evaluate side-chains 424 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 424 time to evaluate : 1.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 150 optimal weight: 0.0050 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 163 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 168 optimal weight: 0.0000 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 221 ASN ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 731 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.081466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.068902 restraints weight = 65110.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.070949 restraints weight = 36041.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072360 restraints weight = 22970.839| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3213 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3213 r_free = 0.3213 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3213 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16581 Z= 0.215 Angle : 0.778 11.079 22523 Z= 0.395 Chirality : 0.048 0.379 2577 Planarity : 0.005 0.064 2917 Dihedral : 5.476 24.601 2239 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.32 % Favored : 89.54 % Rotamer: Outliers : 0.05 % Allowed : 0.33 % Favored : 99.62 % 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: -3.19 (0.18), residues: 2055 helix: -1.01 (0.21), residues: 548 sheet: -1.27 (0.23), residues: 492 loop : -3.29 (0.18), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP X 356 HIS 0.002 0.001 HIS Z 315 PHE 0.025 0.002 PHE Z 742 TYR 0.031 0.002 TYR Z 461 ARG 0.009 0.001 ARG X 618 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4336.45 seconds wall clock time: 79 minutes 50.93 seconds (4790.93 seconds total)