Starting phenix.real_space_refine on Sat Jun 14 15:32:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qtz_18655/06_2025/8qtz_18655.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qtz_18655/06_2025/8qtz_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_18655/06_2025/8qtz_18655.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qtz_18655/06_2025/8qtz_18655.map" model { file = "/net/cci-nas-00/data/ceres_data/8qtz_18655/06_2025/8qtz_18655.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qtz_18655/06_2025/8qtz_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-5710/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: 8.93, per 1000 atoms: 0.55 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: 4.08 Conformation dependent library (CDL) restraints added in 2.7 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: 1.70 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: 4.72 Time building geometry restraints manager: 5.03 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: 19.800 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: 0.860 Check model and map are aligned: 0.170 Set scattering table: 0.140 Process input model: 36.030 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.240 ------------------------------------------------------------------------------- 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= 0.187 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 Details of bonding type rmsd hydrogen bonds : bond 0.21086 ( 473) hydrogen bonds : angle 8.65012 ( 1332) covalent geometry : bond 0.00368 (16581) covalent geometry : angle 0.86314 (22523) *********************** 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 : 1.828 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: 0.2996 time to fit residues: 262.8604 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 : 1.798 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.077018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.064839 restraints weight = 66072.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.066836 restraints weight = 36135.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.068207 restraints weight = 22806.433| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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= 0.212 Angle : 0.787 10.413 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 : 18.74 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 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 473) hydrogen bonds : angle 6.66689 ( 1332) covalent geometry : bond 0.00476 (16581) covalent geometry : angle 0.78725 (22523) *********************** 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 : 1.720 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: 0.8857 (p0) cc_final: 0.8621 (p0) REVERT: X 81 TRP cc_start: 0.7321 (m100) cc_final: 0.5830 (m100) REVERT: X 263 LYS cc_start: 0.8414 (tptt) cc_final: 0.7955 (ttmt) REVERT: X 341 LYS cc_start: 0.7918 (tptt) cc_final: 0.7692 (tppt) REVERT: X 367 TYR cc_start: 0.8452 (m-80) cc_final: 0.7841 (m-80) REVERT: X 414 GLN cc_start: 0.8785 (tp40) cc_final: 0.8551 (tp40) REVERT: X 423 SER cc_start: 0.9196 (t) cc_final: 0.8944 (p) REVERT: X 512 ILE cc_start: 0.9144 (mm) cc_final: 0.8924 (mm) REVERT: X 530 MET cc_start: 0.8631 (ttp) cc_final: 0.8316 (ttp) REVERT: X 531 PHE cc_start: 0.9116 (m-10) cc_final: 0.8572 (m-10) REVERT: X 551 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8769 (ttpt) REVERT: X 575 ILE cc_start: 0.9363 (mm) cc_final: 0.8919 (mp) REVERT: X 635 ASP cc_start: 0.8941 (m-30) cc_final: 0.8678 (m-30) REVERT: X 662 GLU cc_start: 0.8431 (pt0) cc_final: 0.7935 (pt0) REVERT: X 666 LYS cc_start: 0.9229 (mtmm) cc_final: 0.8799 (mtmm) REVERT: X 694 LYS cc_start: 0.8663 (tptp) cc_final: 0.8278 (tptt) REVERT: X 699 GLU cc_start: 0.7968 (mp0) cc_final: 0.7765 (mp0) REVERT: X 707 LYS cc_start: 0.8816 (tptp) cc_final: 0.8333 (tptp) REVERT: X 713 THR cc_start: 0.9297 (t) cc_final: 0.8916 (t) REVERT: X 718 ILE cc_start: 0.9113 (tp) cc_final: 0.8620 (tp) REVERT: X 729 ASN cc_start: 0.9181 (t0) cc_final: 0.8954 (t0) REVERT: X 762 ILE cc_start: 0.8620 (pt) cc_final: 0.8295 (pt) REVERT: X 773 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8224 (tm-30) REVERT: Y 17 ASP cc_start: 0.8759 (p0) cc_final: 0.8250 (p0) REVERT: Y 107 LEU cc_start: 0.8714 (tp) cc_final: 0.7853 (tp) REVERT: Y 271 ILE cc_start: 0.8830 (mm) cc_final: 0.8202 (mm) REVERT: Y 328 PHE cc_start: 0.8522 (t80) cc_final: 0.8253 (t80) REVERT: Y 337 PHE cc_start: 0.8005 (m-80) cc_final: 0.7542 (m-80) REVERT: Y 415 PHE cc_start: 0.7845 (t80) cc_final: 0.7137 (t80) REVERT: Y 527 MET cc_start: 0.8507 (ppp) cc_final: 0.8192 (ppp) REVERT: Y 539 ASP cc_start: 0.7914 (t70) cc_final: 0.7602 (t70) REVERT: Y 549 MET cc_start: 0.7972 (mtm) cc_final: 0.7697 (mmm) REVERT: Y 566 ASP cc_start: 0.8303 (p0) cc_final: 0.8064 (p0) REVERT: Y 619 LEU cc_start: 0.8734 (mm) cc_final: 0.8081 (tp) REVERT: Y 634 ASP cc_start: 0.8026 (p0) cc_final: 0.7263 (p0) REVERT: Y 643 THR cc_start: 0.9313 (m) cc_final: 0.9090 (t) REVERT: Y 645 ILE cc_start: 0.8978 (pt) cc_final: 0.8757 (pt) REVERT: Y 662 GLU cc_start: 0.8924 (pt0) cc_final: 0.8501 (pt0) REVERT: Y 673 TYR cc_start: 0.8287 (m-80) cc_final: 0.7753 (m-10) REVERT: Y 691 PHE cc_start: 0.8862 (m-80) cc_final: 0.8244 (m-80) REVERT: Y 743 ASN cc_start: 0.9083 (m-40) cc_final: 0.8712 (m-40) REVERT: Y 745 LEU cc_start: 0.9524 (mt) cc_final: 0.9216 (mm) REVERT: Y 769 GLN cc_start: 0.7474 (mm110) cc_final: 0.7083 (tp40) REVERT: Y 773 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8478 (tm-30) REVERT: Z 1 MET cc_start: 0.8565 (tmm) cc_final: 0.8005 (tmm) REVERT: Z 5 ILE cc_start: 0.7043 (mm) cc_final: 0.6141 (mm) REVERT: Z 271 ILE cc_start: 0.9287 (tp) cc_final: 0.8557 (tp) REVERT: Z 356 TRP cc_start: 0.7460 (t-100) cc_final: 0.6489 (t-100) REVERT: Z 422 ASN cc_start: 0.8630 (p0) cc_final: 0.8329 (p0) REVERT: Z 454 ASP cc_start: 0.9020 (t70) cc_final: 0.8775 (t0) REVERT: Z 494 LEU cc_start: 0.8426 (mp) cc_final: 0.8194 (tt) REVERT: Z 505 PHE cc_start: 0.8459 (m-80) cc_final: 0.7533 (m-80) REVERT: Z 525 LEU cc_start: 0.8701 (pt) cc_final: 0.8477 (pp) REVERT: Z 611 GLN cc_start: 0.8936 (mp10) cc_final: 0.8396 (mp10) REVERT: Z 623 GLU cc_start: 0.7873 (tp30) cc_final: 0.7092 (mm-30) REVERT: Z 632 ASN cc_start: 0.8548 (t0) cc_final: 0.7958 (t0) REVERT: Z 659 ILE cc_start: 0.9046 (mm) cc_final: 0.8752 (tp) REVERT: Z 674 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7931 (mtm-85) REVERT: Z 689 LYS cc_start: 0.9192 (mmtm) cc_final: 0.8891 (mmmm) REVERT: Z 728 LYS cc_start: 0.6302 (ttpt) cc_final: 0.5988 (tppt) REVERT: Z 740 GLN cc_start: 0.9011 (mt0) cc_final: 0.8779 (mt0) REVERT: Z 754 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8273 (tm-30) REVERT: Z 759 ASP cc_start: 0.8624 (p0) cc_final: 0.8291 (p0) REVERT: Z 764 ARG cc_start: 0.8048 (tpm170) cc_final: 0.6985 (tpm170) REVERT: Z 767 ILE cc_start: 0.9169 (tt) cc_final: 0.8343 (tt) outliers start: 10 outliers final: 2 residues processed: 533 average time/residue: 0.2984 time to fit residues: 228.4708 Evaluate side-chains 444 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 442 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 132 optimal weight: 6.9990 chunk 52 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 182 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** Z 773 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.078015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.065777 restraints weight = 65123.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.067792 restraints weight = 35950.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.069162 restraints weight = 22708.809| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16581 Z= 0.158 Angle : 0.746 10.328 22523 Z= 0.389 Chirality : 0.048 0.246 2577 Planarity : 0.005 0.063 2917 Dihedral : 5.914 24.426 2239 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.95 % Favored : 88.86 % Rotamer: Outliers : 0.11 % Allowed : 4.36 % Favored : 95.53 % 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: -3.60 (0.17), residues: 2055 helix: -1.08 (0.20), residues: 545 sheet: -1.85 (0.24), residues: 413 loop : -3.44 (0.16), residues: 1097 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 0.045 0.002 PHE X 505 TYR 0.027 0.002 TYR X 219 ARG 0.005 0.000 ARG X 753 Details of bonding type rmsd hydrogen bonds : bond 0.04727 ( 473) hydrogen bonds : angle 6.34006 ( 1332) covalent geometry : bond 0.00357 (16581) covalent geometry : angle 0.74585 (22523) *********************** 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 : 1.792 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: 0.8860 (p0) cc_final: 0.8595 (p0) REVERT: X 140 PHE cc_start: 0.7698 (t80) cc_final: 0.7083 (t80) REVERT: X 141 ILE cc_start: 0.8669 (pt) cc_final: 0.8428 (pt) REVERT: X 263 LYS cc_start: 0.8415 (tptt) cc_final: 0.8066 (ttmt) REVERT: X 276 LYS cc_start: 0.8517 (tptp) cc_final: 0.8281 (tttt) REVERT: X 341 LYS cc_start: 0.7620 (tptt) cc_final: 0.7319 (tppt) REVERT: X 367 TYR cc_start: 0.8562 (m-80) cc_final: 0.7793 (m-80) REVERT: X 423 SER cc_start: 0.9127 (t) cc_final: 0.8867 (p) REVERT: X 512 ILE cc_start: 0.9172 (mm) cc_final: 0.8955 (mm) REVERT: X 531 PHE cc_start: 0.9191 (m-10) cc_final: 0.8635 (m-10) REVERT: X 551 LYS cc_start: 0.9196 (ttmt) cc_final: 0.8791 (ttpt) REVERT: X 575 ILE cc_start: 0.9353 (mm) cc_final: 0.8917 (mp) REVERT: X 635 ASP cc_start: 0.8918 (m-30) cc_final: 0.8258 (m-30) REVERT: X 665 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8632 (tm-30) REVERT: X 666 LYS cc_start: 0.9188 (mtmm) cc_final: 0.8688 (mtmm) REVERT: X 693 TYR cc_start: 0.5906 (t80) cc_final: 0.5218 (t80) REVERT: X 694 LYS cc_start: 0.8650 (tptp) cc_final: 0.8211 (tptt) REVERT: X 699 GLU cc_start: 0.8066 (mp0) cc_final: 0.7837 (mp0) REVERT: X 707 LYS cc_start: 0.8827 (tptp) cc_final: 0.8284 (tptp) REVERT: X 713 THR cc_start: 0.9196 (t) cc_final: 0.8876 (t) REVERT: X 718 ILE cc_start: 0.8969 (tp) cc_final: 0.8718 (tp) REVERT: X 729 ASN cc_start: 0.9140 (t0) cc_final: 0.8920 (t0) REVERT: X 762 ILE cc_start: 0.8488 (pt) cc_final: 0.8140 (pt) REVERT: X 773 GLN cc_start: 0.8456 (tm-30) cc_final: 0.8173 (tm-30) REVERT: Y 17 ASP cc_start: 0.8778 (p0) cc_final: 0.8337 (p0) REVERT: Y 29 LYS cc_start: 0.8767 (mmpt) cc_final: 0.8493 (tttt) REVERT: Y 107 LEU cc_start: 0.8735 (tp) cc_final: 0.7927 (tp) REVERT: Y 220 ILE cc_start: 0.7537 (tp) cc_final: 0.7151 (pt) REVERT: Y 271 ILE cc_start: 0.8670 (mm) cc_final: 0.8330 (mm) REVERT: Y 273 ILE cc_start: 0.8715 (tp) cc_final: 0.8208 (tp) REVERT: Y 328 PHE cc_start: 0.8615 (t80) cc_final: 0.8348 (t80) REVERT: Y 337 PHE cc_start: 0.7917 (m-80) cc_final: 0.7495 (m-80) REVERT: Y 415 PHE cc_start: 0.7668 (t80) cc_final: 0.7104 (t80) REVERT: Y 519 ASP cc_start: 0.7549 (m-30) cc_final: 0.7037 (m-30) REVERT: Y 522 LEU cc_start: 0.9200 (tp) cc_final: 0.8969 (tp) REVERT: Y 527 MET cc_start: 0.8456 (ppp) cc_final: 0.8175 (ppp) REVERT: Y 539 ASP cc_start: 0.7954 (t70) cc_final: 0.7585 (t70) REVERT: Y 549 MET cc_start: 0.7844 (mtm) cc_final: 0.7403 (mmm) REVERT: Y 566 ASP cc_start: 0.8266 (p0) cc_final: 0.8050 (p0) REVERT: Y 619 LEU cc_start: 0.8733 (mm) cc_final: 0.7997 (tp) REVERT: Y 634 ASP cc_start: 0.8201 (p0) cc_final: 0.7457 (p0) REVERT: Y 643 THR cc_start: 0.9342 (m) cc_final: 0.9104 (t) REVERT: Y 645 ILE cc_start: 0.8980 (pt) cc_final: 0.8729 (pt) REVERT: Y 662 GLU cc_start: 0.9027 (pt0) cc_final: 0.8373 (pt0) REVERT: Y 673 TYR cc_start: 0.8123 (m-80) cc_final: 0.7523 (m-10) REVERT: Y 680 ASP cc_start: 0.7596 (m-30) cc_final: 0.7375 (m-30) REVERT: Y 707 LYS cc_start: 0.9325 (mmmm) cc_final: 0.9096 (mmmm) REVERT: Y 753 ARG cc_start: 0.7972 (ttt90) cc_final: 0.7723 (ttt90) REVERT: Y 769 GLN cc_start: 0.7484 (mm110) cc_final: 0.7079 (tp40) REVERT: Y 773 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8399 (tm-30) REVERT: Z 1 MET cc_start: 0.8709 (tmm) cc_final: 0.7963 (tmm) REVERT: Z 5 ILE cc_start: 0.6861 (mm) cc_final: 0.5937 (mm) REVERT: Z 356 TRP cc_start: 0.7246 (t-100) cc_final: 0.6298 (t-100) REVERT: Z 422 ASN cc_start: 0.8623 (p0) cc_final: 0.8350 (p0) REVERT: Z 525 LEU cc_start: 0.8814 (pt) cc_final: 0.8524 (pp) REVERT: Z 611 GLN cc_start: 0.8948 (mp10) cc_final: 0.8356 (mp10) REVERT: Z 620 ARG cc_start: 0.8126 (tmt170) cc_final: 0.7884 (tpt90) REVERT: Z 623 GLU cc_start: 0.7665 (tp30) cc_final: 0.6939 (tp30) REVERT: Z 624 MET cc_start: 0.7885 (ptp) cc_final: 0.6350 (ptp) REVERT: Z 631 MET cc_start: 0.8173 (tmm) cc_final: 0.7924 (tmm) REVERT: Z 632 ASN cc_start: 0.8647 (t0) cc_final: 0.8225 (t0) REVERT: Z 659 ILE cc_start: 0.9043 (mm) cc_final: 0.8697 (tp) REVERT: Z 666 LYS cc_start: 0.8990 (mmmm) cc_final: 0.8779 (mppt) REVERT: Z 683 GLU cc_start: 0.7589 (pp20) cc_final: 0.6904 (pp20) REVERT: Z 689 LYS cc_start: 0.9145 (mmtm) cc_final: 0.8796 (mmmm) REVERT: Z 718 ILE cc_start: 0.9153 (mp) cc_final: 0.8916 (mp) REVERT: Z 721 ILE cc_start: 0.9415 (mt) cc_final: 0.8835 (mt) REVERT: Z 728 LYS cc_start: 0.6259 (ttpt) cc_final: 0.6045 (tppt) REVERT: Z 748 ASP cc_start: 0.8969 (t0) cc_final: 0.8767 (t0) REVERT: Z 754 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8216 (tm-30) REVERT: Z 759 ASP cc_start: 0.8538 (p0) cc_final: 0.8232 (p0) REVERT: Z 764 ARG cc_start: 0.8050 (tpm170) cc_final: 0.6885 (tpm170) REVERT: Z 767 ILE cc_start: 0.9171 (tt) cc_final: 0.8482 (tt) outliers start: 2 outliers final: 1 residues processed: 527 average time/residue: 0.3140 time to fit residues: 240.5036 Evaluate side-chains 451 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 126 optimal weight: 0.0770 chunk 6 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 188 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 158 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 overall best weight: 1.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Y 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 324 ASN ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.079070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.066796 restraints weight = 64463.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.068851 restraints weight = 35370.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.070230 restraints weight = 22209.697| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16581 Z= 0.139 Angle : 0.727 10.562 22523 Z= 0.377 Chirality : 0.047 0.215 2577 Planarity : 0.005 0.084 2917 Dihedral : 5.723 24.496 2239 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.19 % Favored : 88.61 % Rotamer: Outliers : 0.05 % Allowed : 4.90 % Favored : 95.04 % 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: -3.47 (0.17), residues: 2055 helix: -0.98 (0.21), residues: 543 sheet: -1.72 (0.25), residues: 423 loop : -3.38 (0.17), residues: 1089 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 0.050 0.002 PHE X 505 TYR 0.022 0.002 TYR Z 461 ARG 0.009 0.001 ARG X 443 Details of bonding type rmsd hydrogen bonds : bond 0.04274 ( 473) hydrogen bonds : angle 6.09506 ( 1332) covalent geometry : bond 0.00312 (16581) covalent geometry : angle 0.72728 (22523) *********************** 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 528 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 527 time to evaluate : 1.659 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 14 TYR cc_start: 0.7462 (p90) cc_final: 0.7104 (p90) REVERT: X 20 ASP cc_start: 0.8803 (p0) cc_final: 0.8541 (p0) REVERT: X 21 GLU cc_start: 0.8453 (pp20) cc_final: 0.8046 (pp20) REVERT: X 25 ILE cc_start: 0.8679 (tp) cc_final: 0.8473 (tp) REVERT: X 81 TRP cc_start: 0.7212 (m100) cc_final: 0.5862 (m100) REVERT: X 140 PHE cc_start: 0.7339 (t80) cc_final: 0.6865 (t80) REVERT: X 141 ILE cc_start: 0.8528 (pt) cc_final: 0.8313 (pt) REVERT: X 142 ASP cc_start: 0.6087 (m-30) cc_final: 0.5282 (m-30) REVERT: X 263 LYS cc_start: 0.8310 (tptt) cc_final: 0.8021 (ttmt) REVERT: X 273 ILE cc_start: 0.8913 (pt) cc_final: 0.8711 (tt) REVERT: X 355 TYR cc_start: 0.8542 (t80) cc_final: 0.8160 (t80) REVERT: X 356 TRP cc_start: 0.5824 (m-10) cc_final: 0.4920 (m-10) REVERT: X 367 TYR cc_start: 0.8550 (m-80) cc_final: 0.7852 (m-80) REVERT: X 423 SER cc_start: 0.9160 (t) cc_final: 0.8882 (p) REVERT: X 504 GLU cc_start: 0.8653 (pp20) cc_final: 0.8444 (pp20) REVERT: X 527 MET cc_start: 0.6873 (mtt) cc_final: 0.6609 (mtt) REVERT: X 530 MET cc_start: 0.8571 (ttm) cc_final: 0.8266 (ttm) REVERT: X 531 PHE cc_start: 0.9188 (m-10) cc_final: 0.8479 (m-10) REVERT: X 544 MET cc_start: 0.9004 (ppp) cc_final: 0.8329 (ppp) REVERT: X 551 LYS cc_start: 0.9070 (ttmt) cc_final: 0.8781 (ttpt) REVERT: X 618 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7595 (ptm-80) REVERT: X 631 MET cc_start: 0.8617 (tpp) cc_final: 0.8245 (tpp) REVERT: X 635 ASP cc_start: 0.8949 (m-30) cc_final: 0.8545 (m-30) REVERT: X 644 LYS cc_start: 0.8760 (tppt) cc_final: 0.8437 (mmmm) REVERT: X 658 ASP cc_start: 0.8330 (p0) cc_final: 0.8104 (p0) REVERT: X 662 GLU cc_start: 0.8241 (pm20) cc_final: 0.7643 (pm20) REVERT: X 665 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8482 (tm-30) REVERT: X 666 LYS cc_start: 0.9137 (mtmm) cc_final: 0.8571 (mtmm) REVERT: X 694 LYS cc_start: 0.8638 (tptp) cc_final: 0.8265 (tptt) REVERT: X 699 GLU cc_start: 0.8036 (mp0) cc_final: 0.7756 (mp0) REVERT: X 703 PHE cc_start: 0.7352 (p90) cc_final: 0.6154 (p90) REVERT: X 707 LYS cc_start: 0.8844 (tptp) cc_final: 0.8559 (tptp) REVERT: X 718 ILE cc_start: 0.9080 (tp) cc_final: 0.8523 (tp) REVERT: X 729 ASN cc_start: 0.9114 (t0) cc_final: 0.8898 (t0) REVERT: X 762 ILE cc_start: 0.8471 (pt) cc_final: 0.8083 (pt) REVERT: X 773 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8302 (tm-30) REVERT: Y 17 ASP cc_start: 0.8842 (p0) cc_final: 0.8441 (p0) REVERT: Y 42 GLN cc_start: 0.9036 (mp10) cc_final: 0.8617 (mp10) REVERT: Y 107 LEU cc_start: 0.8725 (tp) cc_final: 0.7981 (tp) REVERT: Y 220 ILE cc_start: 0.7513 (tp) cc_final: 0.7165 (pt) REVERT: Y 271 ILE cc_start: 0.8744 (mm) cc_final: 0.8477 (mm) REVERT: Y 273 ILE cc_start: 0.8699 (tp) cc_final: 0.8156 (tp) REVERT: Y 328 PHE cc_start: 0.8641 (t80) cc_final: 0.8362 (t80) REVERT: Y 380 CYS cc_start: 0.8732 (m) cc_final: 0.8182 (t) REVERT: Y 415 PHE cc_start: 0.7538 (t80) cc_final: 0.7029 (t80) REVERT: Y 500 GLU cc_start: 0.7313 (pt0) cc_final: 0.6064 (pp20) REVERT: Y 522 LEU cc_start: 0.9198 (tp) cc_final: 0.8954 (tp) REVERT: Y 527 MET cc_start: 0.8456 (ppp) cc_final: 0.8202 (ppp) REVERT: Y 539 ASP cc_start: 0.8027 (t70) cc_final: 0.7688 (t70) REVERT: Y 549 MET cc_start: 0.7841 (mtm) cc_final: 0.7398 (mmm) REVERT: Y 619 LEU cc_start: 0.8746 (mm) cc_final: 0.7974 (tp) REVERT: Y 634 ASP cc_start: 0.7700 (p0) cc_final: 0.7062 (p0) REVERT: Y 643 THR cc_start: 0.9352 (m) cc_final: 0.9119 (t) REVERT: Y 662 GLU cc_start: 0.8919 (pt0) cc_final: 0.8329 (pt0) REVERT: Y 673 TYR cc_start: 0.8106 (m-80) cc_final: 0.7515 (m-10) REVERT: Y 680 ASP cc_start: 0.7586 (m-30) cc_final: 0.7380 (m-30) REVERT: Y 691 PHE cc_start: 0.8664 (m-80) cc_final: 0.8382 (m-80) REVERT: Y 753 ARG cc_start: 0.7830 (ttt90) cc_final: 0.7394 (ttt90) REVERT: Y 769 GLN cc_start: 0.7470 (mm110) cc_final: 0.7088 (tp40) REVERT: Y 773 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8308 (tm-30) REVERT: Z 1 MET cc_start: 0.8559 (tmm) cc_final: 0.7753 (tmm) REVERT: Z 5 ILE cc_start: 0.6826 (mm) cc_final: 0.6039 (mm) REVERT: Z 271 ILE cc_start: 0.9336 (tp) cc_final: 0.8726 (tp) REVERT: Z 273 ILE cc_start: 0.9164 (tp) cc_final: 0.8848 (tp) REVERT: Z 356 TRP cc_start: 0.7401 (t-100) cc_final: 0.7088 (t-100) REVERT: Z 494 LEU cc_start: 0.8481 (mp) cc_final: 0.8184 (tt) REVERT: Z 497 GLN cc_start: 0.7607 (mp10) cc_final: 0.7166 (mp10) REVERT: Z 505 PHE cc_start: 0.8552 (m-80) cc_final: 0.7880 (m-80) REVERT: Z 611 GLN cc_start: 0.8960 (mp10) cc_final: 0.8393 (mp10) REVERT: Z 617 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8458 (ttm110) REVERT: Z 623 GLU cc_start: 0.7678 (tp30) cc_final: 0.6761 (mm-30) REVERT: Z 632 ASN cc_start: 0.8628 (t0) cc_final: 0.8118 (t0) REVERT: Z 658 ASP cc_start: 0.8937 (m-30) cc_final: 0.8171 (m-30) REVERT: Z 662 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7247 (mp0) REVERT: Z 683 GLU cc_start: 0.7745 (pp20) cc_final: 0.7365 (pp20) REVERT: Z 689 LYS cc_start: 0.9021 (mmtm) cc_final: 0.8730 (mmmm) REVERT: Z 721 ILE cc_start: 0.9444 (mt) cc_final: 0.9211 (mp) REVERT: Z 724 PHE cc_start: 0.8296 (t80) cc_final: 0.8094 (t80) REVERT: Z 728 LYS cc_start: 0.6219 (ttpt) cc_final: 0.5826 (tppt) REVERT: Z 748 ASP cc_start: 0.8970 (t0) cc_final: 0.8725 (t0) REVERT: Z 759 ASP cc_start: 0.8499 (p0) cc_final: 0.8139 (p0) REVERT: Z 764 ARG cc_start: 0.8018 (tpm170) cc_final: 0.6862 (tpm170) REVERT: Z 767 ILE cc_start: 0.9150 (tt) cc_final: 0.8498 (tt) outliers start: 1 outliers final: 0 residues processed: 527 average time/residue: 0.2875 time to fit residues: 219.9883 Evaluate side-chains 448 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 37 optimal weight: 0.3980 chunk 140 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 10 optimal weight: 10.0000 chunk 151 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 72 optimal weight: 0.0970 chunk 15 optimal weight: 8.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 8 GLN X 116 ASN X 757 ASN ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 760 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.080554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.068181 restraints weight = 65871.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.070249 restraints weight = 36100.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.071665 restraints weight = 22749.987| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 16581 Z= 0.136 Angle : 0.740 10.013 22523 Z= 0.378 Chirality : 0.047 0.215 2577 Planarity : 0.005 0.070 2917 Dihedral : 5.664 25.531 2239 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.05 % Favored : 88.81 % Rotamer: Outliers : 0.11 % Allowed : 2.94 % Favored : 96.95 % 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: -3.35 (0.17), residues: 2055 helix: -1.01 (0.21), residues: 543 sheet: -1.47 (0.24), residues: 475 loop : -3.37 (0.17), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 81 HIS 0.002 0.001 HIS X 170 PHE 0.054 0.002 PHE X 505 TYR 0.025 0.001 TYR Z 461 ARG 0.010 0.001 ARG X 443 Details of bonding type rmsd hydrogen bonds : bond 0.04117 ( 473) hydrogen bonds : angle 5.96975 ( 1332) covalent geometry : bond 0.00310 (16581) covalent geometry : angle 0.73972 (22523) *********************** 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: 2 poor density : 511 time to evaluate : 1.759 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 20 ASP cc_start: 0.8833 (p0) cc_final: 0.8538 (p0) REVERT: X 21 GLU cc_start: 0.8514 (pp20) cc_final: 0.8313 (pp20) REVERT: X 25 ILE cc_start: 0.8658 (tp) cc_final: 0.8380 (tp) REVERT: X 29 LYS cc_start: 0.9029 (pptt) cc_final: 0.8749 (ptmm) REVERT: X 140 PHE cc_start: 0.7220 (t80) cc_final: 0.6980 (t80) REVERT: X 263 LYS cc_start: 0.8328 (tptt) cc_final: 0.8053 (ttmt) REVERT: X 371 LEU cc_start: 0.7643 (pt) cc_final: 0.7149 (pt) REVERT: X 375 LEU cc_start: 0.8895 (mm) cc_final: 0.8607 (mt) REVERT: X 423 SER cc_start: 0.9158 (t) cc_final: 0.8857 (p) REVERT: X 512 ILE cc_start: 0.9357 (mm) cc_final: 0.9095 (mm) REVERT: X 530 MET cc_start: 0.8644 (ttm) cc_final: 0.8310 (ttm) REVERT: X 531 PHE cc_start: 0.9203 (m-10) cc_final: 0.8529 (m-10) REVERT: X 551 LYS cc_start: 0.9008 (ttmt) cc_final: 0.8762 (ttmt) REVERT: X 658 ASP cc_start: 0.8251 (p0) cc_final: 0.7925 (p0) REVERT: X 665 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8516 (tm-30) REVERT: X 666 LYS cc_start: 0.9149 (mtmm) cc_final: 0.8557 (mtmm) REVERT: X 682 PHE cc_start: 0.8831 (m-10) cc_final: 0.8048 (m-80) REVERT: X 694 LYS cc_start: 0.8644 (tptp) cc_final: 0.8170 (tptt) REVERT: X 699 GLU cc_start: 0.8050 (mp0) cc_final: 0.7811 (mp0) REVERT: X 704 ASP cc_start: 0.8355 (t0) cc_final: 0.8067 (t0) REVERT: X 718 ILE cc_start: 0.8953 (tp) cc_final: 0.8390 (tp) REVERT: X 768 GLU cc_start: 0.8581 (tm-30) cc_final: 0.8358 (tm-30) REVERT: Y 12 ASN cc_start: 0.7851 (m-40) cc_final: 0.7353 (p0) REVERT: Y 17 ASP cc_start: 0.8681 (p0) cc_final: 0.8448 (p0) REVERT: Y 42 GLN cc_start: 0.9013 (mp10) cc_final: 0.8557 (mp10) REVERT: Y 107 LEU cc_start: 0.8788 (tp) cc_final: 0.8103 (tp) REVERT: Y 220 ILE cc_start: 0.7403 (tp) cc_final: 0.7099 (pt) REVERT: Y 271 ILE cc_start: 0.8814 (mm) cc_final: 0.8529 (mm) REVERT: Y 328 PHE cc_start: 0.8612 (t80) cc_final: 0.8358 (t80) REVERT: Y 380 CYS cc_start: 0.8755 (m) cc_final: 0.8114 (t) REVERT: Y 415 PHE cc_start: 0.7595 (t80) cc_final: 0.7015 (t80) REVERT: Y 500 GLU cc_start: 0.7304 (pt0) cc_final: 0.6217 (pp20) REVERT: Y 519 ASP cc_start: 0.7775 (m-30) cc_final: 0.7174 (m-30) REVERT: Y 527 MET cc_start: 0.8420 (ppp) cc_final: 0.8200 (ppp) REVERT: Y 539 ASP cc_start: 0.7956 (t70) cc_final: 0.7691 (t70) REVERT: Y 619 LEU cc_start: 0.8734 (mm) cc_final: 0.8033 (tp) REVERT: Y 624 MET cc_start: 0.8274 (tmm) cc_final: 0.7970 (tmm) REVERT: Y 643 THR cc_start: 0.9352 (m) cc_final: 0.9123 (t) REVERT: Y 645 ILE cc_start: 0.8998 (pt) cc_final: 0.8759 (pt) REVERT: Y 662 GLU cc_start: 0.8908 (pt0) cc_final: 0.8347 (pt0) REVERT: Y 673 TYR cc_start: 0.8091 (m-80) cc_final: 0.7578 (m-10) REVERT: Y 691 PHE cc_start: 0.8779 (m-80) cc_final: 0.8207 (m-80) REVERT: Y 732 ASP cc_start: 0.6887 (t0) cc_final: 0.6465 (t0) REVERT: Y 753 ARG cc_start: 0.7785 (ttt90) cc_final: 0.7506 (ttt90) REVERT: Y 769 GLN cc_start: 0.7444 (mm110) cc_final: 0.6995 (tp40) REVERT: Y 773 GLN cc_start: 0.8742 (tm-30) cc_final: 0.8264 (tm-30) REVERT: Z 1 MET cc_start: 0.8694 (tmm) cc_final: 0.7807 (tmm) REVERT: Z 5 ILE cc_start: 0.6293 (mm) cc_final: 0.5894 (mm) REVERT: Z 8 GLN cc_start: 0.7830 (pm20) cc_final: 0.7245 (pm20) REVERT: Z 263 LYS cc_start: 0.9157 (mppt) cc_final: 0.8938 (mmtm) REVERT: Z 271 ILE cc_start: 0.9263 (tp) cc_final: 0.8903 (tp) REVERT: Z 356 TRP cc_start: 0.7233 (t-100) cc_final: 0.7029 (t-100) REVERT: Z 371 LEU cc_start: 0.9186 (tp) cc_final: 0.8823 (tp) REVERT: Z 497 GLN cc_start: 0.7647 (mp10) cc_final: 0.7227 (mp10) REVERT: Z 505 PHE cc_start: 0.8476 (m-80) cc_final: 0.7894 (m-80) REVERT: Z 514 MET cc_start: 0.7545 (mtp) cc_final: 0.6875 (mtp) REVERT: Z 552 PHE cc_start: 0.7959 (m-80) cc_final: 0.7647 (m-80) REVERT: Z 611 GLN cc_start: 0.8948 (mp10) cc_final: 0.8376 (mp10) REVERT: Z 617 ARG cc_start: 0.8693 (ttm110) cc_final: 0.8483 (ttm110) REVERT: Z 623 GLU cc_start: 0.7306 (tp30) cc_final: 0.6702 (tp30) REVERT: Z 632 ASN cc_start: 0.8364 (t0) cc_final: 0.7563 (p0) REVERT: Z 659 ILE cc_start: 0.8953 (tp) cc_final: 0.8656 (tp) REVERT: Z 689 LYS cc_start: 0.9077 (mmtm) cc_final: 0.8750 (mmmm) REVERT: Z 724 PHE cc_start: 0.8204 (t80) cc_final: 0.7913 (t80) REVERT: Z 728 LYS cc_start: 0.6211 (ttpt) cc_final: 0.5861 (tppt) REVERT: Z 748 ASP cc_start: 0.8957 (t0) cc_final: 0.8641 (t70) REVERT: Z 750 ARG cc_start: 0.8586 (tpp80) cc_final: 0.8200 (tpp80) REVERT: Z 759 ASP cc_start: 0.8498 (p0) cc_final: 0.7971 (p0) REVERT: Z 764 ARG cc_start: 0.7819 (tpm170) cc_final: 0.7576 (tpm170) REVERT: Z 767 ILE cc_start: 0.9099 (tt) cc_final: 0.8697 (tt) outliers start: 2 outliers final: 0 residues processed: 513 average time/residue: 0.2850 time to fit residues: 213.8581 Evaluate side-chains 446 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 22 optimal weight: 0.0570 chunk 178 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 204 optimal weight: 0.9990 chunk 84 optimal weight: 9.9990 chunk 77 optimal weight: 0.0000 chunk 164 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 23 optimal weight: 6.9990 overall best weight: 0.7506 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 8 GLN X 757 ASN ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 739 GLN Z 760 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.080976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.068604 restraints weight = 65468.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.070671 restraints weight = 36081.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.072063 restraints weight = 22724.223| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16581 Z= 0.140 Angle : 0.738 10.214 22523 Z= 0.376 Chirality : 0.048 0.404 2577 Planarity : 0.006 0.142 2917 Dihedral : 5.594 25.976 2239 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.95 % Favored : 88.91 % Rotamer: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.17), residues: 2055 helix: -1.05 (0.21), residues: 550 sheet: -1.38 (0.24), residues: 475 loop : -3.34 (0.17), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 138 HIS 0.002 0.001 HIS X 188 PHE 0.033 0.002 PHE Y 505 TYR 0.025 0.001 TYR Z 461 ARG 0.006 0.001 ARG X 674 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 473) hydrogen bonds : angle 5.82519 ( 1332) covalent geometry : bond 0.00320 (16581) covalent geometry : angle 0.73764 (22523) *********************** 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 509 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 508 time to evaluate : 1.844 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 8 GLN cc_start: 0.8380 (pt0) cc_final: 0.7762 (pp30) REVERT: X 20 ASP cc_start: 0.8889 (p0) cc_final: 0.8628 (p0) REVERT: X 81 TRP cc_start: 0.7290 (m100) cc_final: 0.5564 (m100) REVERT: X 116 ASN cc_start: 0.8287 (t0) cc_final: 0.8049 (t0) REVERT: X 140 PHE cc_start: 0.7200 (t80) cc_final: 0.6897 (t80) REVERT: X 168 MET cc_start: 0.7870 (pmm) cc_final: 0.7446 (pmm) REVERT: X 263 LYS cc_start: 0.8390 (tptt) cc_final: 0.8042 (ttmt) REVERT: X 371 LEU cc_start: 0.7663 (pt) cc_final: 0.7175 (pt) REVERT: X 423 SER cc_start: 0.9144 (t) cc_final: 0.8859 (p) REVERT: X 512 ILE cc_start: 0.9304 (mm) cc_final: 0.9078 (mm) REVERT: X 527 MET cc_start: 0.7318 (mtt) cc_final: 0.4625 (mtt) REVERT: X 530 MET cc_start: 0.8683 (ttm) cc_final: 0.8465 (tpp) REVERT: X 551 LYS cc_start: 0.8990 (ttmt) cc_final: 0.8684 (ttpt) REVERT: X 615 ILE cc_start: 0.9142 (pt) cc_final: 0.8696 (pt) REVERT: X 635 ASP cc_start: 0.8805 (m-30) cc_final: 0.8367 (m-30) REVERT: X 645 ILE cc_start: 0.9245 (tp) cc_final: 0.8858 (pt) REVERT: X 662 GLU cc_start: 0.8277 (pm20) cc_final: 0.7809 (pm20) REVERT: X 665 GLU cc_start: 0.8737 (tm-30) cc_final: 0.8506 (tm-30) REVERT: X 666 LYS cc_start: 0.9094 (mtmm) cc_final: 0.8499 (mtmm) REVERT: X 681 VAL cc_start: 0.7761 (p) cc_final: 0.7522 (p) REVERT: X 694 LYS cc_start: 0.8693 (tptp) cc_final: 0.8296 (tptt) REVERT: X 699 GLU cc_start: 0.8042 (mp0) cc_final: 0.7748 (mp0) REVERT: X 704 ASP cc_start: 0.8378 (t0) cc_final: 0.8045 (t0) REVERT: X 713 THR cc_start: 0.9098 (t) cc_final: 0.8767 (t) REVERT: X 718 ILE cc_start: 0.8908 (tp) cc_final: 0.8655 (tp) REVERT: X 728 LYS cc_start: 0.8869 (mptt) cc_final: 0.8551 (mmtm) REVERT: X 768 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8214 (tm-30) REVERT: Y 12 ASN cc_start: 0.7737 (m-40) cc_final: 0.7398 (p0) REVERT: Y 42 GLN cc_start: 0.8971 (mp10) cc_final: 0.8542 (mp10) REVERT: Y 107 LEU cc_start: 0.8793 (tp) cc_final: 0.8142 (tp) REVERT: Y 220 ILE cc_start: 0.7443 (tp) cc_final: 0.7107 (pt) REVERT: Y 273 ILE cc_start: 0.8888 (tp) cc_final: 0.8619 (tp) REVERT: Y 328 PHE cc_start: 0.8578 (t80) cc_final: 0.8340 (t80) REVERT: Y 337 PHE cc_start: 0.7929 (m-80) cc_final: 0.7570 (m-80) REVERT: Y 380 CYS cc_start: 0.8671 (m) cc_final: 0.8220 (m) REVERT: Y 415 PHE cc_start: 0.7432 (t80) cc_final: 0.6931 (t80) REVERT: Y 471 ILE cc_start: 0.9490 (tp) cc_final: 0.9196 (tp) REVERT: Y 500 GLU cc_start: 0.7380 (pt0) cc_final: 0.6211 (pp20) REVERT: Y 519 ASP cc_start: 0.7812 (m-30) cc_final: 0.7080 (m-30) REVERT: Y 527 MET cc_start: 0.8436 (ppp) cc_final: 0.7674 (tmm) REVERT: Y 539 ASP cc_start: 0.7975 (t70) cc_final: 0.7710 (t0) REVERT: Y 619 LEU cc_start: 0.8708 (mm) cc_final: 0.8343 (tp) REVERT: Y 634 ASP cc_start: 0.8191 (p0) cc_final: 0.7209 (p0) REVERT: Y 662 GLU cc_start: 0.8901 (pt0) cc_final: 0.8330 (pt0) REVERT: Y 673 TYR cc_start: 0.8103 (m-80) cc_final: 0.7600 (m-80) REVERT: Y 680 ASP cc_start: 0.7921 (m-30) cc_final: 0.7618 (m-30) REVERT: Y 691 PHE cc_start: 0.8768 (m-80) cc_final: 0.8045 (m-80) REVERT: Y 753 ARG cc_start: 0.7763 (ttt90) cc_final: 0.7420 (ttt90) REVERT: Y 769 GLN cc_start: 0.7435 (mm110) cc_final: 0.7012 (tp40) REVERT: Y 773 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8209 (tm-30) REVERT: Z 1 MET cc_start: 0.8663 (tmm) cc_final: 0.7785 (tmm) REVERT: Z 5 ILE cc_start: 0.6498 (mm) cc_final: 0.5904 (mm) REVERT: Z 271 ILE cc_start: 0.9449 (tp) cc_final: 0.8945 (tp) REVERT: Z 302 GLN cc_start: 0.8112 (pp30) cc_final: 0.7880 (pp30) REVERT: Z 371 LEU cc_start: 0.9180 (tp) cc_final: 0.8820 (tp) REVERT: Z 497 GLN cc_start: 0.7915 (mp10) cc_final: 0.7598 (mp10) REVERT: Z 505 PHE cc_start: 0.8511 (m-80) cc_final: 0.7896 (m-80) REVERT: Z 514 MET cc_start: 0.7439 (mtp) cc_final: 0.6919 (mtp) REVERT: Z 549 MET cc_start: 0.7993 (mmp) cc_final: 0.7603 (mmp) REVERT: Z 611 GLN cc_start: 0.8949 (mp10) cc_final: 0.8485 (mp10) REVERT: Z 617 ARG cc_start: 0.8723 (ttm110) cc_final: 0.8501 (ttm110) REVERT: Z 623 GLU cc_start: 0.7326 (tp30) cc_final: 0.6689 (tp30) REVERT: Z 632 ASN cc_start: 0.8466 (t0) cc_final: 0.7694 (p0) REVERT: Z 659 ILE cc_start: 0.8811 (tp) cc_final: 0.8578 (tp) REVERT: Z 683 GLU cc_start: 0.7527 (pp20) cc_final: 0.7153 (pp20) REVERT: Z 689 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8779 (mmmm) REVERT: Z 691 PHE cc_start: 0.9129 (m-10) cc_final: 0.8929 (m-10) REVERT: Z 724 PHE cc_start: 0.8142 (t80) cc_final: 0.7786 (t80) REVERT: Z 748 ASP cc_start: 0.9003 (t0) cc_final: 0.8618 (t70) REVERT: Z 754 GLU cc_start: 0.8271 (pt0) cc_final: 0.7895 (pt0) REVERT: Z 759 ASP cc_start: 0.8303 (p0) cc_final: 0.7915 (p0) REVERT: Z 764 ARG cc_start: 0.7805 (tpm170) cc_final: 0.7522 (tpm170) REVERT: Z 767 ILE cc_start: 0.9085 (tt) cc_final: 0.8671 (tt) outliers start: 1 outliers final: 0 residues processed: 509 average time/residue: 0.2867 time to fit residues: 213.3415 Evaluate side-chains 455 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 45 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 38 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 79 optimal weight: 0.0570 chunk 100 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 129 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 0.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 8 GLN X 757 ASN ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 315 HIS ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.081267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.068907 restraints weight = 65022.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.070956 restraints weight = 35848.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.072361 restraints weight = 22708.194| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16581 Z= 0.139 Angle : 0.747 10.363 22523 Z= 0.380 Chirality : 0.047 0.278 2577 Planarity : 0.006 0.071 2917 Dihedral : 5.534 24.990 2239 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.15 % Allowed : 11.19 % Favored : 88.66 % Rotamer: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.17), residues: 2055 helix: -1.02 (0.21), residues: 558 sheet: -1.56 (0.23), residues: 508 loop : -3.30 (0.18), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 356 HIS 0.002 0.001 HIS Y 188 PHE 0.026 0.002 PHE Z 742 TYR 0.023 0.001 TYR Z 305 ARG 0.015 0.001 ARG X 674 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 473) hydrogen bonds : angle 5.81285 ( 1332) covalent geometry : bond 0.00319 (16581) covalent geometry : angle 0.74698 (22523) *********************** 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 511 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 509 time to evaluate : 1.727 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: symmetry clash REVERT: X 116 ASN cc_start: 0.8313 (t0) cc_final: 0.8003 (t0) REVERT: X 140 PHE cc_start: 0.7048 (t80) cc_final: 0.6835 (t80) REVERT: X 141 ILE cc_start: 0.8418 (pt) cc_final: 0.8184 (pt) REVERT: X 356 TRP cc_start: 0.5504 (m-10) cc_final: 0.4799 (m-10) REVERT: X 375 LEU cc_start: 0.8916 (mm) cc_final: 0.8621 (mt) REVERT: X 423 SER cc_start: 0.9146 (t) cc_final: 0.8889 (p) REVERT: X 631 MET cc_start: 0.8784 (tpp) cc_final: 0.8336 (tpp) REVERT: X 645 ILE cc_start: 0.9253 (tp) cc_final: 0.8842 (pt) REVERT: X 665 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8418 (tm-30) REVERT: X 666 LYS cc_start: 0.9037 (mtmm) cc_final: 0.8514 (mtmm) REVERT: X 693 TYR cc_start: 0.5456 (t80) cc_final: 0.5228 (t80) REVERT: X 694 LYS cc_start: 0.8781 (tptp) cc_final: 0.8334 (tptp) REVERT: X 696 ASP cc_start: 0.8811 (t0) cc_final: 0.8566 (t0) REVERT: X 699 GLU cc_start: 0.8040 (mp0) cc_final: 0.7762 (mp0) REVERT: X 704 ASP cc_start: 0.8380 (t0) cc_final: 0.8079 (t0) REVERT: X 728 LYS cc_start: 0.8812 (mptt) cc_final: 0.8535 (mmtm) REVERT: Y 4 LEU cc_start: 0.7102 (pt) cc_final: 0.6343 (pt) REVERT: Y 8 GLN cc_start: 0.8343 (mp10) cc_final: 0.8100 (mp10) REVERT: Y 12 ASN cc_start: 0.7664 (m-40) cc_final: 0.7357 (p0) REVERT: Y 17 ASP cc_start: 0.8736 (p0) cc_final: 0.8331 (p0) REVERT: Y 106 ILE cc_start: 0.8547 (tp) cc_final: 0.8213 (tp) REVERT: Y 107 LEU cc_start: 0.8780 (tp) cc_final: 0.8423 (tp) REVERT: Y 220 ILE cc_start: 0.7649 (tp) cc_final: 0.7264 (pt) REVERT: Y 273 ILE cc_start: 0.8894 (tp) cc_final: 0.8538 (tp) REVERT: Y 328 PHE cc_start: 0.8549 (t80) cc_final: 0.8330 (t80) REVERT: Y 337 PHE cc_start: 0.7885 (m-80) cc_final: 0.7476 (m-80) REVERT: Y 380 CYS cc_start: 0.8699 (m) cc_final: 0.8234 (m) REVERT: Y 415 PHE cc_start: 0.7509 (t80) cc_final: 0.7009 (t80) REVERT: Y 471 ILE cc_start: 0.9512 (tp) cc_final: 0.9248 (tp) REVERT: Y 500 GLU cc_start: 0.6738 (pt0) cc_final: 0.5865 (pp20) REVERT: Y 519 ASP cc_start: 0.7777 (m-30) cc_final: 0.6856 (m-30) REVERT: Y 527 MET cc_start: 0.8517 (ppp) cc_final: 0.8219 (ppp) REVERT: Y 539 ASP cc_start: 0.7989 (t70) cc_final: 0.7703 (t70) REVERT: Y 619 LEU cc_start: 0.8748 (mm) cc_final: 0.8461 (tp) REVERT: Y 634 ASP cc_start: 0.7984 (p0) cc_final: 0.7146 (p0) REVERT: Y 662 GLU cc_start: 0.8904 (pt0) cc_final: 0.8327 (pt0) REVERT: Y 680 ASP cc_start: 0.7910 (m-30) cc_final: 0.7624 (m-30) REVERT: Y 691 PHE cc_start: 0.8908 (m-80) cc_final: 0.8050 (m-80) REVERT: Y 753 ARG cc_start: 0.7727 (ttt90) cc_final: 0.7344 (ttt90) REVERT: Y 769 GLN cc_start: 0.7475 (mm110) cc_final: 0.7013 (tp40) REVERT: Y 773 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8292 (tm-30) REVERT: Z 1 MET cc_start: 0.8652 (tmm) cc_final: 0.8451 (tmm) REVERT: Z 5 ILE cc_start: 0.6537 (mm) cc_final: 0.5909 (mm) REVERT: Z 302 GLN cc_start: 0.8162 (pp30) cc_final: 0.7957 (pp30) REVERT: Z 356 TRP cc_start: 0.7318 (t-100) cc_final: 0.6713 (t-100) REVERT: Z 371 LEU cc_start: 0.9176 (tp) cc_final: 0.8817 (tp) REVERT: Z 494 LEU cc_start: 0.8423 (mp) cc_final: 0.8180 (tt) REVERT: Z 497 GLN cc_start: 0.8066 (mp10) cc_final: 0.7633 (mp10) REVERT: Z 505 PHE cc_start: 0.8482 (m-80) cc_final: 0.7889 (m-80) REVERT: Z 514 MET cc_start: 0.7571 (mtp) cc_final: 0.7104 (mtp) REVERT: Z 611 GLN cc_start: 0.8972 (mp10) cc_final: 0.8505 (mp10) REVERT: Z 623 GLU cc_start: 0.7367 (tp30) cc_final: 0.6703 (tp30) REVERT: Z 632 ASN cc_start: 0.8467 (t0) cc_final: 0.7454 (p0) REVERT: Z 659 ILE cc_start: 0.8809 (tp) cc_final: 0.8559 (tp) REVERT: Z 683 GLU cc_start: 0.7486 (pp20) cc_final: 0.7067 (pp20) REVERT: Z 689 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8757 (mmmm) REVERT: Z 691 PHE cc_start: 0.9137 (m-10) cc_final: 0.8839 (m-10) REVERT: Z 724 PHE cc_start: 0.8145 (t80) cc_final: 0.7890 (t80) REVERT: Z 748 ASP cc_start: 0.9019 (t0) cc_final: 0.8635 (t70) REVERT: Z 754 GLU cc_start: 0.8310 (pt0) cc_final: 0.8015 (pt0) REVERT: Z 759 ASP cc_start: 0.8273 (p0) cc_final: 0.7943 (p0) REVERT: Z 764 ARG cc_start: 0.7785 (tpm170) cc_final: 0.7390 (tpm170) REVERT: Z 767 ILE cc_start: 0.9091 (tt) cc_final: 0.8664 (tt) outliers start: 2 outliers final: 0 residues processed: 510 average time/residue: 0.2871 time to fit residues: 214.5152 Evaluate side-chains 450 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 450 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 83 optimal weight: 3.9990 chunk 31 optimal weight: 0.0270 chunk 52 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 90 optimal weight: 30.0000 chunk 13 optimal weight: 9.9990 chunk 169 optimal weight: 9.9990 chunk 146 optimal weight: 0.2980 chunk 164 optimal weight: 4.9990 chunk 84 optimal weight: 0.0870 chunk 65 optimal weight: 5.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 221 ASN ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 597 GLN Y 731 ASN Z 324 ASN Z 348 ASN Z 739 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.081935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.069486 restraints weight = 64598.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.071558 restraints weight = 35838.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.072946 restraints weight = 22623.220| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3871 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= 0.135 Angle : 0.752 11.496 22523 Z= 0.381 Chirality : 0.047 0.358 2577 Planarity : 0.005 0.059 2917 Dihedral : 5.420 25.668 2239 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.07 % Favored : 89.78 % Rotamer: Outliers : 0.16 % Allowed : 1.53 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.17), residues: 2055 helix: -0.95 (0.21), residues: 553 sheet: -1.27 (0.24), residues: 448 loop : -3.29 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP X 356 HIS 0.002 0.001 HIS X 170 PHE 0.031 0.002 PHE X 505 TYR 0.032 0.001 TYR Z 461 ARG 0.010 0.001 ARG Y 750 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 473) hydrogen bonds : angle 5.71054 ( 1332) covalent geometry : bond 0.00310 (16581) covalent geometry : angle 0.75186 (22523) *********************** 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 513 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 510 time to evaluate : 1.754 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: symmetry clash REVERT: X 20 ASP cc_start: 0.8767 (p0) cc_final: 0.8541 (p0) REVERT: X 21 GLU cc_start: 0.8319 (pp20) cc_final: 0.8074 (tm-30) REVERT: X 25 ILE cc_start: 0.8644 (tp) cc_final: 0.8310 (tp) REVERT: X 81 TRP cc_start: 0.7280 (m100) cc_final: 0.5503 (m100) REVERT: X 116 ASN cc_start: 0.8423 (t0) cc_final: 0.8104 (t0) REVERT: X 140 PHE cc_start: 0.7020 (t80) cc_final: 0.6636 (t80) REVERT: X 142 ASP cc_start: 0.5566 (m-30) cc_final: 0.4929 (m-30) REVERT: X 168 MET cc_start: 0.7907 (pmm) cc_final: 0.7365 (pmm) REVERT: X 371 LEU cc_start: 0.7581 (pt) cc_final: 0.7173 (pt) REVERT: X 423 SER cc_start: 0.9130 (t) cc_final: 0.8850 (p) REVERT: X 512 ILE cc_start: 0.9267 (mm) cc_final: 0.9007 (mm) REVERT: X 530 MET cc_start: 0.8923 (tpt) cc_final: 0.8622 (tpp) REVERT: X 551 LYS cc_start: 0.9243 (ttmt) cc_final: 0.8804 (ttpt) REVERT: X 631 MET cc_start: 0.8624 (tpp) cc_final: 0.8185 (tpp) REVERT: X 645 ILE cc_start: 0.9227 (tp) cc_final: 0.8808 (pt) REVERT: X 665 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8489 (tm-30) REVERT: X 666 LYS cc_start: 0.9078 (mtmm) cc_final: 0.8463 (mtmm) REVERT: X 690 PHE cc_start: 0.8181 (p90) cc_final: 0.7827 (p90) REVERT: X 694 LYS cc_start: 0.8809 (tptp) cc_final: 0.8374 (tptt) REVERT: X 696 ASP cc_start: 0.8788 (t0) cc_final: 0.8518 (t0) REVERT: X 699 GLU cc_start: 0.8038 (mp0) cc_final: 0.7721 (mp0) REVERT: X 710 ASP cc_start: 0.8127 (p0) cc_final: 0.7751 (m-30) REVERT: X 718 ILE cc_start: 0.9040 (tp) cc_final: 0.8653 (tp) REVERT: Y 4 LEU cc_start: 0.7221 (pt) cc_final: 0.6481 (pt) REVERT: Y 8 GLN cc_start: 0.8432 (mp10) cc_final: 0.8057 (mp10) REVERT: Y 12 ASN cc_start: 0.7935 (m-40) cc_final: 0.7674 (p0) REVERT: Y 17 ASP cc_start: 0.8768 (p0) cc_final: 0.8336 (p0) REVERT: Y 107 LEU cc_start: 0.8745 (tp) cc_final: 0.8264 (tp) REVERT: Y 220 ILE cc_start: 0.7632 (tp) cc_final: 0.7292 (pt) REVERT: Y 273 ILE cc_start: 0.8899 (tp) cc_final: 0.8288 (tp) REVERT: Y 380 CYS cc_start: 0.8628 (m) cc_final: 0.7948 (t) REVERT: Y 415 PHE cc_start: 0.7481 (t80) cc_final: 0.6968 (t80) REVERT: Y 463 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7538 (mm-30) REVERT: Y 471 ILE cc_start: 0.9493 (tp) cc_final: 0.9173 (tp) REVERT: Y 500 GLU cc_start: 0.6185 (pt0) cc_final: 0.5256 (pp20) REVERT: Y 519 ASP cc_start: 0.7739 (m-30) cc_final: 0.6790 (m-30) REVERT: Y 527 MET cc_start: 0.8495 (ppp) cc_final: 0.8193 (ppp) REVERT: Y 619 LEU cc_start: 0.8793 (mm) cc_final: 0.8243 (tp) REVERT: Y 634 ASP cc_start: 0.7949 (p0) cc_final: 0.7130 (p0) REVERT: Y 662 GLU cc_start: 0.8910 (pt0) cc_final: 0.8331 (pt0) REVERT: Y 673 TYR cc_start: 0.7954 (m-80) cc_final: 0.7694 (m-80) REVERT: Y 680 ASP cc_start: 0.7906 (m-30) cc_final: 0.7606 (m-30) REVERT: Y 691 PHE cc_start: 0.8775 (m-80) cc_final: 0.7888 (m-80) REVERT: Y 753 ARG cc_start: 0.7725 (ttt90) cc_final: 0.7427 (ttt90) REVERT: Y 769 GLN cc_start: 0.7313 (mm110) cc_final: 0.6857 (tp40) REVERT: Y 772 MET cc_start: 0.7507 (tmm) cc_final: 0.7250 (tmm) REVERT: Y 773 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8102 (tm-30) REVERT: Z 1 MET cc_start: 0.8586 (tmm) cc_final: 0.8101 (tmm) REVERT: Z 5 ILE cc_start: 0.6067 (mm) cc_final: 0.5681 (mt) REVERT: Z 8 GLN cc_start: 0.7479 (pm20) cc_final: 0.7219 (pm20) REVERT: Z 271 ILE cc_start: 0.9306 (tp) cc_final: 0.8760 (tp) REVERT: Z 302 GLN cc_start: 0.8225 (pp30) cc_final: 0.7984 (pp30) REVERT: Z 371 LEU cc_start: 0.9165 (tp) cc_final: 0.8773 (tp) REVERT: Z 497 GLN cc_start: 0.7983 (mp10) cc_final: 0.7590 (mp10) REVERT: Z 505 PHE cc_start: 0.8381 (m-80) cc_final: 0.7749 (m-80) REVERT: Z 514 MET cc_start: 0.7478 (mtp) cc_final: 0.6832 (mtp) REVERT: Z 528 PHE cc_start: 0.8366 (t80) cc_final: 0.8114 (t80) REVERT: Z 623 GLU cc_start: 0.7265 (tp30) cc_final: 0.6693 (mm-30) REVERT: Z 632 ASN cc_start: 0.8485 (t0) cc_final: 0.7428 (p0) REVERT: Z 659 ILE cc_start: 0.8843 (tp) cc_final: 0.8561 (tp) REVERT: Z 674 ARG cc_start: 0.8991 (ptp-110) cc_final: 0.8505 (ptp90) REVERT: Z 724 PHE cc_start: 0.8196 (t80) cc_final: 0.7965 (t80) REVERT: Z 739 GLN cc_start: 0.8053 (tp40) cc_final: 0.7776 (tp40) REVERT: Z 748 ASP cc_start: 0.9161 (t0) cc_final: 0.8773 (t70) REVERT: Z 754 GLU cc_start: 0.8290 (pt0) cc_final: 0.8007 (pt0) REVERT: Z 759 ASP cc_start: 0.8265 (p0) cc_final: 0.7965 (p0) REVERT: Z 764 ARG cc_start: 0.7534 (tpm170) cc_final: 0.7161 (tpm170) REVERT: Z 767 ILE cc_start: 0.9072 (tt) cc_final: 0.8636 (tt) outliers start: 3 outliers final: 1 residues processed: 512 average time/residue: 0.2938 time to fit residues: 221.9198 Evaluate side-chains 458 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 457 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 18 optimal weight: 10.0000 chunk 108 optimal weight: 8.9990 chunk 43 optimal weight: 0.0060 chunk 80 optimal weight: 0.0570 chunk 61 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 177 optimal weight: 0.0670 chunk 144 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 chunk 178 optimal weight: 0.6980 overall best weight: 0.3052 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 221 ASN ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 597 GLN Z 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.083376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.070847 restraints weight = 64559.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.072947 restraints weight = 35698.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.074366 restraints weight = 22557.734| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4066 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= 0.135 Angle : 0.773 11.853 22523 Z= 0.388 Chirality : 0.048 0.302 2577 Planarity : 0.005 0.065 2917 Dihedral : 5.370 26.018 2239 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.22 % Favored : 89.64 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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 (0.17), residues: 2055 helix: -1.03 (0.21), residues: 558 sheet: -1.08 (0.25), residues: 453 loop : -3.34 (0.17), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP X 356 HIS 0.002 0.001 HIS Z 315 PHE 0.033 0.002 PHE X 505 TYR 0.029 0.002 TYR Z 461 ARG 0.012 0.001 ARG X 443 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 473) hydrogen bonds : angle 5.74616 ( 1332) covalent geometry : bond 0.00306 (16581) covalent geometry : angle 0.77342 (22523) *********************** 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 500 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 1.763 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: symmetry clash revert: symmetry clash REVERT: X 20 ASP cc_start: 0.8774 (p0) cc_final: 0.8555 (p0) REVERT: X 21 GLU cc_start: 0.8277 (pp20) cc_final: 0.7956 (tm-30) REVERT: X 24 GLU cc_start: 0.8713 (pp20) cc_final: 0.8496 (tm-30) REVERT: X 25 ILE cc_start: 0.8299 (tp) cc_final: 0.8041 (tp) REVERT: X 116 ASN cc_start: 0.8485 (t0) cc_final: 0.8148 (t0) REVERT: X 140 PHE cc_start: 0.7040 (t80) cc_final: 0.6824 (t80) REVERT: X 142 ASP cc_start: 0.5451 (m-30) cc_final: 0.4750 (m-30) REVERT: X 371 LEU cc_start: 0.7574 (pt) cc_final: 0.7196 (pt) REVERT: X 375 LEU cc_start: 0.8920 (mm) cc_final: 0.8626 (mt) REVERT: X 423 SER cc_start: 0.9091 (t) cc_final: 0.8865 (p) REVERT: X 508 LEU cc_start: 0.9504 (pp) cc_final: 0.9298 (pp) REVERT: X 530 MET cc_start: 0.8940 (tpt) cc_final: 0.8686 (tpp) REVERT: X 551 LYS cc_start: 0.9201 (ttmt) cc_final: 0.8797 (ttpt) REVERT: X 631 MET cc_start: 0.8687 (tpp) cc_final: 0.8370 (tpp) REVERT: X 645 ILE cc_start: 0.9222 (tp) cc_final: 0.8808 (pt) REVERT: X 665 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8385 (tm-30) REVERT: X 666 LYS cc_start: 0.9091 (mtmm) cc_final: 0.8407 (mtmm) REVERT: X 690 PHE cc_start: 0.8176 (p90) cc_final: 0.7837 (p90) REVERT: X 694 LYS cc_start: 0.8819 (tptp) cc_final: 0.8353 (tptt) REVERT: X 696 ASP cc_start: 0.8729 (t0) cc_final: 0.8466 (t0) REVERT: X 699 GLU cc_start: 0.8039 (mp0) cc_final: 0.7745 (mp0) REVERT: X 710 ASP cc_start: 0.8075 (p0) cc_final: 0.7734 (m-30) REVERT: Y 4 LEU cc_start: 0.7131 (pt) cc_final: 0.6338 (pt) REVERT: Y 8 GLN cc_start: 0.8525 (mp10) cc_final: 0.8259 (mp10) REVERT: Y 17 ASP cc_start: 0.8769 (p0) cc_final: 0.8521 (p0) REVERT: Y 107 LEU cc_start: 0.8716 (tp) cc_final: 0.8459 (tp) REVERT: Y 175 TYR cc_start: 0.6594 (m-10) cc_final: 0.6145 (m-10) REVERT: Y 178 GLU cc_start: 0.8555 (pp20) cc_final: 0.8317 (pm20) REVERT: Y 220 ILE cc_start: 0.7755 (tp) cc_final: 0.7025 (pt) REVERT: Y 337 PHE cc_start: 0.7962 (m-80) cc_final: 0.7379 (m-80) REVERT: Y 380 CYS cc_start: 0.8675 (m) cc_final: 0.7977 (t) REVERT: Y 412 SER cc_start: 0.8782 (m) cc_final: 0.8384 (p) REVERT: Y 415 PHE cc_start: 0.7395 (t80) cc_final: 0.6935 (t80) REVERT: Y 463 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7669 (mm-30) REVERT: Y 471 ILE cc_start: 0.9460 (tp) cc_final: 0.9221 (tp) REVERT: Y 500 GLU cc_start: 0.6145 (pt0) cc_final: 0.5220 (pp20) REVERT: Y 519 ASP cc_start: 0.7697 (m-30) cc_final: 0.6724 (m-30) REVERT: Y 527 MET cc_start: 0.8518 (ppp) cc_final: 0.8202 (ppp) REVERT: Y 596 THR cc_start: 0.8881 (p) cc_final: 0.8430 (t) REVERT: Y 634 ASP cc_start: 0.7789 (p0) cc_final: 0.7088 (p0) REVERT: Y 662 GLU cc_start: 0.8928 (pt0) cc_final: 0.8359 (pt0) REVERT: Y 673 TYR cc_start: 0.8023 (m-80) cc_final: 0.7731 (m-80) REVERT: Y 680 ASP cc_start: 0.7861 (m-30) cc_final: 0.7297 (m-30) REVERT: Y 691 PHE cc_start: 0.8828 (m-80) cc_final: 0.7819 (m-80) REVERT: Y 753 ARG cc_start: 0.7714 (ttt90) cc_final: 0.7412 (ttt90) REVERT: Y 769 GLN cc_start: 0.7290 (mm110) cc_final: 0.6824 (tp40) REVERT: Y 772 MET cc_start: 0.7423 (tmm) cc_final: 0.7164 (tmm) REVERT: Y 773 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8097 (tm-30) REVERT: Z 1 MET cc_start: 0.8630 (tmm) cc_final: 0.8400 (tmm) REVERT: Z 5 ILE cc_start: 0.5702 (mm) cc_final: 0.5242 (mt) REVERT: Z 8 GLN cc_start: 0.7405 (pm20) cc_final: 0.7172 (pm20) REVERT: Z 271 ILE cc_start: 0.9418 (tp) cc_final: 0.8926 (tp) REVERT: Z 300 ASN cc_start: 0.8981 (p0) cc_final: 0.8665 (p0) REVERT: Z 356 TRP cc_start: 0.7025 (t-100) cc_final: 0.6334 (t-100) REVERT: Z 371 LEU cc_start: 0.9147 (tp) cc_final: 0.8759 (tp) REVERT: Z 497 GLN cc_start: 0.8164 (mp10) cc_final: 0.7755 (mm-40) REVERT: Z 505 PHE cc_start: 0.8329 (m-80) cc_final: 0.7836 (m-80) REVERT: Z 514 MET cc_start: 0.7461 (mtp) cc_final: 0.6830 (mtp) REVERT: Z 528 PHE cc_start: 0.8352 (t80) cc_final: 0.7989 (t80) REVERT: Z 623 GLU cc_start: 0.7239 (tp30) cc_final: 0.6627 (mm-30) REVERT: Z 632 ASN cc_start: 0.8301 (t0) cc_final: 0.7083 (p0) REVERT: Z 659 ILE cc_start: 0.8825 (tp) cc_final: 0.8553 (tp) REVERT: Z 674 ARG cc_start: 0.8899 (ptp-110) cc_final: 0.8564 (ptp90) REVERT: Z 683 GLU cc_start: 0.7432 (pp20) cc_final: 0.7066 (pp20) REVERT: Z 689 LYS cc_start: 0.9109 (mmtp) cc_final: 0.8803 (mmmm) REVERT: Z 691 PHE cc_start: 0.9066 (m-10) cc_final: 0.8816 (m-10) REVERT: Z 724 PHE cc_start: 0.8135 (t80) cc_final: 0.7875 (t80) REVERT: Z 739 GLN cc_start: 0.8201 (tp40) cc_final: 0.7993 (tp40) REVERT: Z 748 ASP cc_start: 0.9136 (t0) cc_final: 0.8755 (t70) REVERT: Z 754 GLU cc_start: 0.8261 (pt0) cc_final: 0.7972 (pt0) REVERT: Z 755 PHE cc_start: 0.8944 (t80) cc_final: 0.8273 (t80) REVERT: Z 759 ASP cc_start: 0.8376 (p0) cc_final: 0.8099 (p0) REVERT: Z 763 ILE cc_start: 0.9204 (pt) cc_final: 0.8878 (pt) REVERT: Z 764 ARG cc_start: 0.7625 (tpm170) cc_final: 0.7265 (tpm170) REVERT: Z 767 ILE cc_start: 0.9044 (tt) cc_final: 0.8581 (tt) outliers start: 0 outliers final: 0 residues processed: 500 average time/residue: 0.2835 time to fit residues: 209.9208 Evaluate side-chains 436 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 436 time to evaluate : 1.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 39 optimal weight: 8.9990 chunk 172 optimal weight: 0.8980 chunk 152 optimal weight: 0.0570 chunk 199 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 197 optimal weight: 0.7980 chunk 167 optimal weight: 8.9990 chunk 92 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 74 optimal weight: 0.0370 chunk 19 optimal weight: 6.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 221 ASN ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 266 GLN ** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.083423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.070802 restraints weight = 64738.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072911 restraints weight = 36176.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.074342 restraints weight = 22999.239| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16581 Z= 0.131 Angle : 0.759 11.699 22523 Z= 0.383 Chirality : 0.047 0.270 2577 Planarity : 0.005 0.064 2917 Dihedral : 5.278 26.056 2239 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.98 % Favored : 89.88 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % 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: -3.17 (0.17), residues: 2055 helix: -0.96 (0.21), residues: 557 sheet: -1.19 (0.24), residues: 467 loop : -3.31 (0.17), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP X 356 HIS 0.002 0.001 HIS Z 315 PHE 0.035 0.001 PHE X 505 TYR 0.026 0.001 TYR Z 461 ARG 0.008 0.001 ARG Y 750 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 473) hydrogen bonds : angle 5.61869 ( 1332) covalent geometry : bond 0.00301 (16581) covalent geometry : angle 0.75905 (22523) ********************** 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 499 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 1.915 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 21 GLU cc_start: 0.8331 (pp20) cc_final: 0.7863 (tm-30) REVERT: X 25 ILE cc_start: 0.8164 (tp) cc_final: 0.7931 (tp) REVERT: X 116 ASN cc_start: 0.8516 (t0) cc_final: 0.8173 (t0) REVERT: X 140 PHE cc_start: 0.6892 (t80) cc_final: 0.6672 (t80) REVERT: X 141 ILE cc_start: 0.8384 (pt) cc_final: 0.8101 (pt) REVERT: X 142 ASP cc_start: 0.5363 (m-30) cc_final: 0.4650 (m-30) REVERT: X 371 LEU cc_start: 0.7563 (pt) cc_final: 0.7206 (pt) REVERT: X 375 LEU cc_start: 0.8918 (mm) cc_final: 0.8615 (mt) REVERT: X 508 LEU cc_start: 0.9506 (pp) cc_final: 0.9277 (pp) REVERT: X 530 MET cc_start: 0.8977 (tpt) cc_final: 0.8673 (tpp) REVERT: X 551 LYS cc_start: 0.9205 (ttmt) cc_final: 0.8782 (ttpt) REVERT: X 631 MET cc_start: 0.8494 (tpp) cc_final: 0.8105 (tpp) REVERT: X 645 ILE cc_start: 0.9250 (tp) cc_final: 0.8865 (pt) REVERT: X 665 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8445 (tm-30) REVERT: X 666 LYS cc_start: 0.9093 (mtmm) cc_final: 0.8421 (mtmm) REVERT: X 690 PHE cc_start: 0.8255 (p90) cc_final: 0.7908 (p90) REVERT: X 694 LYS cc_start: 0.8820 (tptp) cc_final: 0.8350 (tptt) REVERT: X 696 ASP cc_start: 0.8711 (t0) cc_final: 0.8408 (t0) REVERT: X 699 GLU cc_start: 0.8054 (mp0) cc_final: 0.7745 (mp0) REVERT: X 710 ASP cc_start: 0.8079 (p0) cc_final: 0.7797 (m-30) REVERT: Y 8 GLN cc_start: 0.8587 (mp10) cc_final: 0.8306 (mp10) REVERT: Y 22 ILE cc_start: 0.9082 (pt) cc_final: 0.8863 (pt) REVERT: Y 141 ILE cc_start: 0.8478 (pt) cc_final: 0.8272 (pt) REVERT: Y 207 ILE cc_start: 0.8051 (pt) cc_final: 0.7815 (pt) REVERT: Y 220 ILE cc_start: 0.7810 (tp) cc_final: 0.7541 (pt) REVERT: Y 273 ILE cc_start: 0.8583 (tp) cc_final: 0.8087 (tp) REVERT: Y 275 PHE cc_start: 0.8005 (t80) cc_final: 0.7737 (t80) REVERT: Y 337 PHE cc_start: 0.7851 (m-80) cc_final: 0.7264 (m-80) REVERT: Y 380 CYS cc_start: 0.8675 (m) cc_final: 0.7983 (t) REVERT: Y 412 SER cc_start: 0.8825 (m) cc_final: 0.8607 (p) REVERT: Y 415 PHE cc_start: 0.7411 (t80) cc_final: 0.6953 (t80) REVERT: Y 471 ILE cc_start: 0.9481 (tp) cc_final: 0.9156 (tp) REVERT: Y 500 GLU cc_start: 0.6164 (pt0) cc_final: 0.5268 (pp20) REVERT: Y 519 ASP cc_start: 0.7615 (m-30) cc_final: 0.6572 (m-30) REVERT: Y 527 MET cc_start: 0.8472 (ppp) cc_final: 0.8100 (ppp) REVERT: Y 634 ASP cc_start: 0.7879 (p0) cc_final: 0.7222 (p0) REVERT: Y 662 GLU cc_start: 0.8937 (pt0) cc_final: 0.8354 (pt0) REVERT: Y 673 TYR cc_start: 0.7939 (m-80) cc_final: 0.7673 (m-80) REVERT: Y 680 ASP cc_start: 0.7652 (m-30) cc_final: 0.7440 (m-30) REVERT: Y 691 PHE cc_start: 0.8696 (m-80) cc_final: 0.7700 (m-80) REVERT: Y 753 ARG cc_start: 0.7740 (ttt90) cc_final: 0.7468 (ttt90) REVERT: Y 769 GLN cc_start: 0.7258 (mm110) cc_final: 0.6893 (tp40) REVERT: Y 772 MET cc_start: 0.7421 (tmm) cc_final: 0.7173 (tmm) REVERT: Y 773 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8120 (tm-30) REVERT: Z 1 MET cc_start: 0.8616 (tmm) cc_final: 0.8385 (tmm) REVERT: Z 271 ILE cc_start: 0.9429 (tp) cc_final: 0.8902 (tp) REVERT: Z 300 ASN cc_start: 0.8801 (p0) cc_final: 0.8574 (p0) REVERT: Z 329 ASN cc_start: 0.9232 (t0) cc_final: 0.9018 (t0) REVERT: Z 356 TRP cc_start: 0.6971 (t-100) cc_final: 0.6159 (t-100) REVERT: Z 371 LEU cc_start: 0.9133 (tp) cc_final: 0.8744 (tp) REVERT: Z 494 LEU cc_start: 0.8706 (mp) cc_final: 0.8447 (tt) REVERT: Z 497 GLN cc_start: 0.8048 (mp10) cc_final: 0.7740 (mm-40) REVERT: Z 505 PHE cc_start: 0.8355 (m-80) cc_final: 0.7850 (m-80) REVERT: Z 514 MET cc_start: 0.7477 (mtp) cc_final: 0.6930 (mtp) REVERT: Z 528 PHE cc_start: 0.8279 (t80) cc_final: 0.8009 (t80) REVERT: Z 623 GLU cc_start: 0.7379 (tp30) cc_final: 0.6727 (mm-30) REVERT: Z 632 ASN cc_start: 0.8327 (t0) cc_final: 0.7119 (p0) REVERT: Z 659 ILE cc_start: 0.8859 (tp) cc_final: 0.8596 (tp) REVERT: Z 674 ARG cc_start: 0.8866 (ptp-110) cc_final: 0.8541 (ptp90) REVERT: Z 689 LYS cc_start: 0.9172 (mmtp) cc_final: 0.8865 (mmmm) REVERT: Z 706 GLN cc_start: 0.7956 (pm20) cc_final: 0.7744 (pm20) REVERT: Z 739 GLN cc_start: 0.8107 (tp40) cc_final: 0.7846 (tp40) REVERT: Z 748 ASP cc_start: 0.9202 (t0) cc_final: 0.8779 (t70) REVERT: Z 754 GLU cc_start: 0.8271 (pt0) cc_final: 0.7978 (pp20) REVERT: Z 755 PHE cc_start: 0.8949 (t80) cc_final: 0.8337 (t80) REVERT: Z 759 ASP cc_start: 0.8384 (p0) cc_final: 0.8132 (p0) REVERT: Z 763 ILE cc_start: 0.9271 (pt) cc_final: 0.8831 (pt) REVERT: Z 764 ARG cc_start: 0.7650 (tpm170) cc_final: 0.7214 (tpm170) REVERT: Z 767 ILE cc_start: 0.9045 (tt) cc_final: 0.8622 (tt) outliers start: 0 outliers final: 0 residues processed: 499 average time/residue: 0.3137 time to fit residues: 234.1135 Evaluate side-chains 447 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 73 optimal weight: 0.9980 chunk 189 optimal weight: 8.9990 chunk 173 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 152 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 X 611 GLN ** X 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.090556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.077704 restraints weight = 64284.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.079811 restraints weight = 36172.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081257 restraints weight = 23078.915| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4322 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= 0.139 Angle : 0.771 11.504 22523 Z= 0.388 Chirality : 0.047 0.242 2577 Planarity : 0.005 0.065 2917 Dihedral : 5.268 25.695 2239 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.15 % Allowed : 10.80 % Favored : 89.05 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: -3.11 (0.18), residues: 2055 helix: -0.87 (0.21), residues: 553 sheet: -1.31 (0.23), residues: 484 loop : -3.23 (0.18), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP X 356 HIS 0.002 0.001 HIS Z 315 PHE 0.034 0.002 PHE X 505 TYR 0.051 0.002 TYR Z 673 ARG 0.009 0.001 ARG X 7 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 473) hydrogen bonds : angle 5.61781 ( 1332) covalent geometry : bond 0.00323 (16581) covalent geometry : angle 0.77068 (22523) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6489.02 seconds wall clock time: 113 minutes 29.21 seconds (6809.21 seconds total)