Starting phenix.real_space_refine on Mon Nov 18 23:21:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ole_16956/11_2024/8ole_16956.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ole_16956/11_2024/8ole_16956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ole_16956/11_2024/8ole_16956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ole_16956/11_2024/8ole_16956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ole_16956/11_2024/8ole_16956.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ole_16956/11_2024/8ole_16956.cif" } resolution = 4.4 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= 0.067 sd= 0.425 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 57 5.16 5 C 11209 2.51 5 N 2976 2.21 5 O 3515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17757 Number of models: 1 Model: "" Number of chains: 3 Chain: "X" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6107 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 35, 'TRANS': 740} Chain: "Y" Number of atoms: 6107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 6107 Classifications: {'peptide': 776} Link IDs: {'PTRANS': 35, 'TRANS': 740} Chain: "Z" Number of atoms: 5543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5543 Classifications: {'peptide': 702} Link IDs: {'PTRANS': 25, 'TRANS': 676} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY Y 156 " occ=0.65 ... (2 atoms not shown) pdb=" O GLY Y 156 " occ=0.65 residue: pdb=" N GLY Z 156 " occ=0.98 ... (2 atoms not shown) pdb=" O GLY Z 156 " occ=0.98 Time building chain proxies: 9.65, per 1000 atoms: 0.54 Number of scatterers: 17757 At special positions: 0 Unit cell: (115.24, 93.8, 210.38, 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 57 16.00 O 3515 8.00 N 2976 7.00 C 11209 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: 4.43 Conformation dependent library (CDL) restraints added in 2.4 seconds 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4280 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 32 sheets defined 28.7% alpha, 15.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 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 193 through 197 removed outlier: 4.015A pdb=" N SER X 196 " --> pdb=" O ASN X 193 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VAL X 197 " --> pdb=" O TYR X 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 193 through 197' Processing helix chain 'X' and resid 212 through 222 removed outlier: 3.966A pdb=" N CYS X 216 " --> pdb=" O GLU X 212 " (cutoff:3.500A) Processing helix chain 'X' and resid 359 through 365 removed outlier: 4.128A pdb=" N ARG X 363 " --> pdb=" O SER X 359 " (cutoff:3.500A) Processing helix chain 'X' and resid 494 through 510 removed outlier: 3.997A pdb=" N GLU X 500 " --> pdb=" O ARG X 496 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU X 503 " --> pdb=" O GLY X 499 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU X 504 " --> pdb=" O GLU X 500 " (cutoff:3.500A) Processing helix chain 'X' and resid 515 through 520 removed outlier: 3.549A pdb=" N ASP X 519 " --> pdb=" O SER X 515 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 531 Processing helix chain 'X' and resid 540 through 553 removed outlier: 3.792A pdb=" N LYS X 553 " --> pdb=" O MET X 549 " (cutoff:3.500A) Processing helix chain 'X' and resid 555 through 573 removed outlier: 3.560A pdb=" N ASN X 559 " --> pdb=" O SER X 555 " (cutoff:3.500A) Processing helix chain 'X' and resid 593 through 597 removed outlier: 3.666A pdb=" N GLN X 597 " --> pdb=" O VAL X 594 " (cutoff:3.500A) Processing helix chain 'X' and resid 606 through 626 removed outlier: 3.913A pdb=" N ARG X 618 " --> pdb=" O THR X 614 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU X 621 " --> pdb=" O ARG X 617 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA X 625 " --> pdb=" O LEU X 621 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR X 626 " --> pdb=" O LYS X 622 " (cutoff:3.500A) Processing helix chain 'X' and resid 632 through 647 removed outlier: 3.838A pdb=" N ILE X 636 " --> pdb=" O ASN X 632 " (cutoff:3.500A) Processing helix chain 'X' and resid 655 through 667 removed outlier: 3.867A pdb=" N GLU X 665 " --> pdb=" O THR X 661 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 715 removed outlier: 4.129A pdb=" N ASP X 714 " --> pdb=" O ASP X 710 " (cutoff:3.500A) Processing helix chain 'X' and resid 723 through 731 Processing helix chain 'X' and resid 738 through 745 Processing helix chain 'X' and resid 748 through 759 removed outlier: 3.702A pdb=" N GLN X 758 " --> pdb=" O GLU X 754 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP X 759 " --> pdb=" O PHE X 755 " (cutoff:3.500A) Processing helix chain 'X' and resid 761 through 776 removed outlier: 4.521A pdb=" N ASN X 765 " --> pdb=" O PRO X 761 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU X 776 " --> pdb=" O MET X 772 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 12 removed outlier: 3.896A pdb=" N LEU Y 10 " --> pdb=" O TYR Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 29 Processing helix chain 'Y' and resid 120 through 124 Processing helix chain 'Y' and resid 182 through 184 No H-bonds generated for 'chain 'Y' and resid 182 through 184' 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 497 through 510 Processing helix chain 'Y' and resid 514 through 522 Processing helix chain 'Y' and resid 539 through 553 removed outlier: 3.758A pdb=" N LYS Y 553 " --> pdb=" O MET Y 549 " (cutoff:3.500A) Processing helix chain 'Y' and resid 555 through 574 removed outlier: 3.744A pdb=" N SER Y 574 " --> pdb=" O ASP Y 570 " (cutoff:3.500A) Processing helix chain 'Y' and resid 589 through 594 Processing helix chain 'Y' and resid 607 through 619 Processing helix chain 'Y' and resid 620 through 625 Processing helix chain 'Y' and resid 632 through 647 removed outlier: 3.722A pdb=" N ILE Y 636 " --> pdb=" O ASN Y 632 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA Y 639 " --> pdb=" O ASP Y 635 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS Y 647 " --> pdb=" O THR Y 643 " (cutoff:3.500A) Processing helix chain 'Y' and resid 659 through 667 Processing helix chain 'Y' and resid 704 through 713 Processing helix chain 'Y' and resid 723 through 734 Processing helix chain 'Y' and resid 737 through 747 removed outlier: 3.568A pdb=" N ARG Y 746 " --> pdb=" O PHE Y 742 " (cutoff:3.500A) Processing helix chain 'Y' and resid 748 through 758 removed outlier: 4.263A pdb=" N LEU Y 752 " --> pdb=" O ASP Y 748 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLN Y 758 " --> pdb=" O GLU Y 754 " (cutoff:3.500A) Processing helix chain 'Y' and resid 762 through 774 removed outlier: 4.176A pdb=" N ARG Y 766 " --> pdb=" O ILE Y 762 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU Y 768 " --> pdb=" O ARG Y 764 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS Y 774 " --> pdb=" O LEU Y 770 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 12 Processing helix chain 'Z' and resid 15 through 27 removed outlier: 3.872A pdb=" N GLN Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing helix chain 'Z' and resid 193 through 197 removed outlier: 3.640A pdb=" N VAL Z 197 " --> pdb=" O TYR Z 194 " (cutoff:3.500A) Processing helix chain 'Z' and resid 212 through 221 Processing helix chain 'Z' and resid 359 through 364 removed outlier: 3.618A pdb=" N ARG Z 363 " --> pdb=" O SER Z 359 " (cutoff:3.500A) Processing helix chain 'Z' and resid 497 through 507 removed outlier: 3.967A pdb=" N GLU Z 503 " --> pdb=" O GLY Z 499 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLU Z 504 " --> pdb=" O GLU Z 500 " (cutoff:3.500A) Processing helix chain 'Z' and resid 515 through 521 Processing helix chain 'Z' and resid 526 through 531 Processing helix chain 'Z' and resid 540 through 552 removed outlier: 3.519A pdb=" N MET Z 544 " --> pdb=" O ALA Z 540 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N MET Z 549 " --> pdb=" O ALA Z 545 " (cutoff:3.500A) Processing helix chain 'Z' and resid 557 through 572 Processing helix chain 'Z' and resid 589 through 594 removed outlier: 3.616A pdb=" N ASP Z 593 " --> pdb=" O SER Z 589 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL Z 594 " --> pdb=" O ALA Z 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 589 through 594' Processing helix chain 'Z' and resid 606 through 624 Processing helix chain 'Z' and resid 632 through 647 Processing helix chain 'Z' and resid 655 through 660 removed outlier: 3.636A pdb=" N ILE Z 659 " --> pdb=" O THR Z 655 " (cutoff:3.500A) Processing helix chain 'Z' and resid 660 through 665 Processing helix chain 'Z' and resid 704 through 714 Processing helix chain 'Z' and resid 723 through 733 Processing helix chain 'Z' and resid 737 through 746 Processing helix chain 'Z' and resid 748 through 760 removed outlier: 3.769A pdb=" N ASP Z 759 " --> pdb=" O PHE Z 755 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN Z 760 " --> pdb=" O ILE Z 756 " (cutoff:3.500A) Processing helix chain 'Z' and resid 761 through 773 Processing sheet with id=AA1, first strand: chain 'X' and resid 73 through 74 removed outlier: 4.211A pdb=" N ILE X 92 " --> pdb=" O THR X 105 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N THR X 105 " --> pdb=" O ILE X 92 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N GLU X 94 " --> pdb=" O LEU X 103 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU X 103 " --> pdb=" O GLU X 94 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N PHE X 140 " --> pdb=" O SER X 157 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER X 157 " --> pdb=" O PHE X 140 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'X' and resid 165 through 166 removed outlier: 3.515A pdb=" N TYR X 165 " --> pdb=" O LEU X 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 115 through 121 Processing sheet with id=AA4, first strand: chain 'X' and resid 175 through 180 Processing sheet with id=AA5, first strand: chain 'X' and resid 254 through 257 removed outlier: 6.955A pdb=" N GLU Y 264 " --> pdb=" O ILE X 256 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE Y 273 " --> pdb=" O ILE Y 464 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE Y 464 " --> pdb=" O ILE Y 273 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N LEU Y 473 " --> pdb=" O VAL Y 368 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N VAL Y 368 " --> pdb=" O LEU Y 473 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'X' and resid 270 through 274 Processing sheet with id=AA7, first strand: chain 'X' and resid 278 through 283 removed outlier: 3.735A pdb=" N ALA X 278 " --> pdb=" O LYS X 297 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER X 295 " --> pdb=" O THR X 280 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N TRP X 291 " --> pdb=" O SER X 340 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N PHE X 342 " --> pdb=" O TRP X 291 " (cutoff:3.500A) removed outlier: 9.244A pdb=" N GLU X 293 " --> pdb=" O PHE X 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 300 through 307 removed outlier: 3.742A pdb=" N TYR X 303 " --> pdb=" O ALA X 314 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'X' and resid 354 through 357 current: chain 'X' and resid 402 through 415 removed outlier: 5.868A pdb=" N ARG X 427 " --> pdb=" O ALA X 407 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL X 409 " --> pdb=" O ARG X 425 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ARG X 425 " --> pdb=" O VAL X 409 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N LEU X 411 " --> pdb=" O SER X 423 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N SER X 423 " --> pdb=" O LEU X 411 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR X 413 " --> pdb=" O LEU X 421 " (cutoff:3.500A) removed outlier: 6.056A 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 315 through 321 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 350 through 354 current: chain 'Y' and resid 419 through 423 Processing sheet with id=AA9, first strand: chain 'X' and resid 323 through 324 Processing sheet with id=AB1, first strand: chain 'X' and resid 384 through 386 Processing sheet with id=AB2, first strand: chain 'X' and resid 680 through 683 removed outlier: 3.773A pdb=" N ASN X 677 " --> pdb=" O ASP X 680 " (cutoff:3.500A) Processing sheet with id=AB3, 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 297 WARNING: can't find start of bonding for strands! previous: chain 'Z' and resid 290 through 297 current: chain 'Z' and resid 338 through 345 Processing sheet with id=AB4, first strand: chain 'Y' and resid 165 through 166 removed outlier: 3.529A pdb=" N TYR Y 165 " --> pdb=" O LEU Y 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 139 through 145 removed outlier: 3.728A pdb=" N LYS Y 139 " --> pdb=" O ILE Y 108 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE Y 108 " --> pdb=" O LYS Y 139 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR Y 105 " --> pdb=" O VAL Y 93 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N VAL Y 93 " --> pdb=" O THR Y 105 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LEU Y 107 " --> pdb=" O VAL Y 91 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL Y 91 " --> pdb=" O LEU Y 107 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 115 through 116 Processing sheet with id=AB7, first strand: chain 'Y' and resid 158 through 159 Processing sheet with id=AB8, first strand: chain 'Y' and resid 290 through 291 removed outlier: 3.713A pdb=" N PHE Y 328 " --> pdb=" O VAL Y 339 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'Y' and resid 306 through 307 Processing sheet with id=AC1, first strand: chain 'Y' and resid 628 through 629 removed outlier: 3.850A pdb=" N GLU Y 629 " --> pdb=" O VAL Y 717 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER Y 719 " --> pdb=" O GLU Y 629 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Z' and resid 80 through 81 removed outlier: 3.896A pdb=" N ILE Z 208 " --> pdb=" O TRP Z 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Z' and resid 83 through 84 removed outlier: 6.368A pdb=" N ALA Z 166 " --> pdb=" O TYR Z 177 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR Z 177 " --> pdb=" O ALA Z 166 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N MET Z 168 " --> pdb=" O TYR Z 175 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR Z 175 " --> pdb=" O MET Z 168 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Z' and resid 93 through 96 Processing sheet with id=AC5, first strand: chain 'Z' and resid 102 through 108 removed outlier: 3.513A pdb=" N ALA Z 104 " --> pdb=" O VAL Z 143 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS Z 139 " --> pdb=" O ILE Z 108 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N GLY Z 156 " --> pdb=" O ASP Z 142 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL Z 144 " --> pdb=" O GLN Z 154 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLN Z 154 " --> pdb=" O VAL Z 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 112 through 116 removed outlier: 3.565A pdb=" N VAL Z 112 " --> pdb=" O ASN Z 132 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER Z 114 " --> pdb=" O VAL Z 130 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N VAL Z 130 " --> pdb=" O SER Z 114 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 120 through 121 Processing sheet with id=AC8, first strand: chain 'Z' and resid 263 through 264 removed outlier: 3.540A pdb=" N LYS Z 263 " --> pdb=" O VAL Z 474 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL Z 474 " --> pdb=" O LYS Z 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'Z' and resid 267 through 268 Processing sheet with id=AD1, first strand: chain 'Z' and resid 273 through 275 Processing sheet with id=AD2, first strand: chain 'Z' and resid 302 through 307 Processing sheet with id=AD3, first strand: chain 'Z' and resid 319 through 321 removed outlier: 3.566A pdb=" N ASN Z 321 " --> pdb=" O TYR Z 350 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR Z 350 " --> pdb=" O ASN Z 321 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL Z 351 " --> pdb=" O PHE Z 428 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LEU Z 421 " --> pdb=" O THR Z 413 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N THR Z 413 " --> pdb=" O LEU Z 421 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N SER Z 423 " --> pdb=" O LEU Z 411 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N LEU Z 411 " --> pdb=" O SER Z 423 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ARG Z 425 " --> pdb=" O VAL Z 409 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N VAL Z 409 " --> pdb=" O ARG Z 425 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG Z 427 " --> pdb=" O ALA Z 407 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 381 through 382 Processing sheet with id=AD5, first strand: chain 'Z' and resid 690 through 692 removed outlier: 3.838A pdb=" N PHE Z 682 " --> pdb=" O VAL Z 675 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL Z 675 " --> pdb=" O PHE Z 682 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1524 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: 6.39 Time building geometry restraints manager: 5.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3727 1.33 - 1.45: 4211 1.45 - 1.57: 10079 1.57 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 18116 Sorted by residual: bond pdb=" N GLU Y 434 " pdb=" CA GLU Y 434 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.04e-02 9.25e+03 1.16e+01 bond pdb=" N HIS Y 436 " pdb=" CA HIS Y 436 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.27e-02 6.20e+03 8.87e+00 bond pdb=" N THR X 181 " pdb=" CA THR X 181 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.41e-02 5.03e+03 6.71e+00 bond pdb=" N ARG Z 620 " pdb=" CA ARG Z 620 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.19e-02 7.06e+03 6.66e+00 bond pdb=" N TRP Z 102 " pdb=" CA TRP Z 102 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.22e-02 6.72e+03 6.55e+00 ... (remaining 18111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.20: 24306 3.20 - 6.40: 283 6.40 - 9.60: 34 9.60 - 12.80: 1 12.80 - 16.00: 2 Bond angle restraints: 24626 Sorted by residual: angle pdb=" C THR Y 181 " pdb=" CA THR Y 181 " pdb=" CB THR Y 181 " ideal model delta sigma weight residual 110.17 126.17 -16.00 1.97e+00 2.58e-01 6.59e+01 angle pdb=" C THR X 181 " pdb=" CA THR X 181 " pdb=" CB THR X 181 " ideal model delta sigma weight residual 110.17 125.30 -15.13 1.97e+00 2.58e-01 5.90e+01 angle pdb=" C GLU Z 495 " pdb=" CA GLU Z 495 " pdb=" CB GLU Z 495 " ideal model delta sigma weight residual 115.79 108.69 7.10 1.19e+00 7.06e-01 3.56e+01 angle pdb=" C ARG Z 620 " pdb=" CA ARG Z 620 " pdb=" CB ARG Z 620 " ideal model delta sigma weight residual 110.88 103.40 7.48 1.57e+00 4.06e-01 2.27e+01 angle pdb=" C ASN X 229 " pdb=" N THR X 230 " pdb=" CA THR X 230 " ideal model delta sigma weight residual 122.08 129.02 -6.94 1.47e+00 4.63e-01 2.23e+01 ... (remaining 24621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 9885 17.95 - 35.91: 853 35.91 - 53.86: 139 53.86 - 71.81: 26 71.81 - 89.77: 10 Dihedral angle restraints: 10913 sinusoidal: 4291 harmonic: 6622 Sorted by residual: dihedral pdb=" C THR Y 181 " pdb=" N THR Y 181 " pdb=" CA THR Y 181 " pdb=" CB THR Y 181 " ideal model delta harmonic sigma weight residual -122.00 -148.18 26.18 0 2.50e+00 1.60e-01 1.10e+02 dihedral pdb=" C THR X 181 " pdb=" N THR X 181 " pdb=" CA THR X 181 " pdb=" CB THR X 181 " ideal model delta harmonic sigma weight residual -122.00 -141.11 19.11 0 2.50e+00 1.60e-01 5.84e+01 dihedral pdb=" N THR Y 181 " pdb=" C THR Y 181 " pdb=" CA THR Y 181 " pdb=" CB THR Y 181 " ideal model delta harmonic sigma weight residual 123.40 142.46 -19.06 0 2.50e+00 1.60e-01 5.82e+01 ... (remaining 10910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 2806 0.185 - 0.371: 12 0.371 - 0.556: 0 0.556 - 0.741: 1 0.741 - 0.927: 1 Chirality restraints: 2820 Sorted by residual: chirality pdb=" CA THR Y 181 " pdb=" N THR Y 181 " pdb=" C THR Y 181 " pdb=" CB THR Y 181 " both_signs ideal model delta sigma weight residual False 2.53 1.60 0.93 2.00e-01 2.50e+01 2.15e+01 chirality pdb=" CA THR X 181 " pdb=" N THR X 181 " pdb=" C THR X 181 " pdb=" CB THR X 181 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" CB ILE Z 686 " pdb=" CA ILE Z 686 " pdb=" CG1 ILE Z 686 " pdb=" CG2 ILE Z 686 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 2817 not shown) Planarity restraints: 3186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY X 67 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.01e+00 pdb=" N PRO X 68 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO X 68 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO X 68 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP Y 100 " -0.014 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C ASP Y 100 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP Y 100 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG Y 101 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU X 389 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO X 390 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO X 390 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO X 390 " -0.038 5.00e-02 4.00e+02 ... (remaining 3183 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 43 2.22 - 2.89: 7678 2.89 - 3.56: 28015 3.56 - 4.23: 43419 4.23 - 4.90: 68983 Nonbonded interactions: 148138 Sorted by model distance: nonbonded pdb=" NH2 ARG Z 620 " pdb=" O ALA Z 684 " model vdw 1.554 3.120 nonbonded pdb=" CB ASP Y 714 " pdb=" NH1 ARG Z 750 " model vdw 1.808 3.520 nonbonded pdb=" O GLU Y 347 " pdb=" CZ ARG Y 429 " model vdw 1.931 3.270 nonbonded pdb=" OG SER Y 161 " pdb=" CG2 THR Y 181 " model vdw 2.023 3.460 nonbonded pdb=" OE1 GLU Y 347 " pdb=" NH2 ARG Y 429 " model vdw 2.028 3.120 ... (remaining 148133 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' and (resid 1 through 29 or resid 73 through 221 or resid 253 through \ 776)) selection = (chain 'Y' and (resid 1 through 29 or resid 73 through 221 or resid 253 through \ 776)) selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 39.700 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 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 0.053 18116 Z= 0.257 Angle : 0.902 15.997 24626 Z= 0.507 Chirality : 0.057 0.927 2820 Planarity : 0.006 0.076 3186 Dihedral : 13.976 89.766 6633 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 30.06 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.61 % Favored : 87.08 % Rotamer: Outliers : 0.15 % Allowed : 0.50 % Favored : 99.35 % Cbeta Deviations : 0.09 % 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: -3.85 (0.16), residues: 2244 helix: -1.31 (0.20), residues: 566 sheet: -2.39 (0.21), residues: 527 loop : -3.37 (0.16), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP X 356 HIS 0.009 0.002 HIS Y 315 PHE 0.023 0.002 PHE X 505 TYR 0.042 0.002 TYR X 219 ARG 0.008 0.001 ARG X 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 440 time to evaluate : 1.747 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: symmetry clash REVERT: X 1 MET cc_start: 0.7339 (mmm) cc_final: 0.7093 (mmm) REVERT: X 10 LEU cc_start: 0.8545 (tt) cc_final: 0.8323 (tt) REVERT: X 18 LEU cc_start: 0.8166 (mt) cc_final: 0.7959 (mt) REVERT: X 40 PHE cc_start: 0.7288 (p90) cc_final: 0.6762 (p90) REVERT: X 100 ASP cc_start: 0.6010 (t0) cc_final: 0.5800 (t0) REVERT: X 219 TYR cc_start: 0.8100 (m-80) cc_final: 0.7567 (m-80) REVERT: X 222 ASN cc_start: 0.8331 (m-40) cc_final: 0.7958 (p0) REVERT: X 242 ASP cc_start: 0.8032 (t0) cc_final: 0.7758 (t0) REVERT: X 265 MET cc_start: 0.3859 (mpp) cc_final: 0.3402 (mpp) REVERT: X 291 TRP cc_start: 0.7283 (m-10) cc_final: 0.6825 (m-10) REVERT: X 296 PHE cc_start: 0.7621 (m-10) cc_final: 0.7362 (m-10) REVERT: X 317 THR cc_start: 0.6420 (m) cc_final: 0.6205 (m) REVERT: X 333 LEU cc_start: 0.8836 (tt) cc_final: 0.8523 (mt) REVERT: X 347 GLU cc_start: 0.8419 (mt-10) cc_final: 0.8009 (mm-30) REVERT: X 410 THR cc_start: 0.8058 (m) cc_final: 0.7362 (p) REVERT: X 447 LEU cc_start: 0.8069 (tp) cc_final: 0.7826 (tt) REVERT: X 494 LEU cc_start: 0.9137 (tp) cc_final: 0.8668 (tp) REVERT: X 527 MET cc_start: 0.6973 (mtm) cc_final: 0.6484 (mtm) REVERT: X 530 MET cc_start: 0.7645 (ptt) cc_final: 0.7250 (ptt) REVERT: X 531 PHE cc_start: 0.8250 (m-80) cc_final: 0.7769 (m-80) REVERT: X 544 MET cc_start: 0.7588 (mmp) cc_final: 0.7361 (mmp) REVERT: X 552 PHE cc_start: 0.8230 (t80) cc_final: 0.7508 (t80) REVERT: X 615 ILE cc_start: 0.8266 (pt) cc_final: 0.7946 (mt) REVERT: X 667 PHE cc_start: 0.7364 (m-10) cc_final: 0.6384 (m-10) REVERT: X 727 LEU cc_start: 0.8577 (mp) cc_final: 0.8366 (mt) REVERT: X 755 PHE cc_start: 0.7833 (m-80) cc_final: 0.7185 (m-10) REVERT: X 772 MET cc_start: 0.8498 (mtm) cc_final: 0.7799 (mtm) REVERT: X 773 GLN cc_start: 0.8853 (pt0) cc_final: 0.8625 (pt0) REVERT: X 774 CYS cc_start: 0.5812 (p) cc_final: 0.5592 (p) REVERT: Y 5 ILE cc_start: 0.8433 (mt) cc_final: 0.7956 (mt) REVERT: Y 75 ASN cc_start: 0.8126 (p0) cc_final: 0.7804 (p0) REVERT: Y 94 GLU cc_start: 0.7743 (tt0) cc_final: 0.7083 (tm-30) REVERT: Y 116 ASN cc_start: 0.7853 (m-40) cc_final: 0.7265 (t0) REVERT: Y 128 LEU cc_start: 0.7082 (tt) cc_final: 0.6537 (pp) REVERT: Y 142 ASP cc_start: 0.7332 (t0) cc_final: 0.6876 (t0) REVERT: Y 170 HIS cc_start: 0.7993 (t70) cc_final: 0.7605 (t70) REVERT: Y 297 LYS cc_start: 0.8350 (mmpt) cc_final: 0.8112 (mmtm) REVERT: Y 350 TYR cc_start: 0.7503 (m-10) cc_final: 0.6476 (m-10) REVERT: Y 371 LEU cc_start: 0.8169 (pt) cc_final: 0.7945 (pt) REVERT: Y 414 GLN cc_start: 0.6920 (mp10) cc_final: 0.6035 (mp10) REVERT: Y 422 ASN cc_start: 0.7937 (t0) cc_final: 0.7368 (t0) REVERT: Y 444 LEU cc_start: 0.8513 (tp) cc_final: 0.7891 (pp) REVERT: Y 530 MET cc_start: 0.7663 (tpt) cc_final: 0.6931 (tpt) REVERT: Y 591 TRP cc_start: 0.8047 (m-90) cc_final: 0.7306 (m-90) REVERT: Y 617 ARG cc_start: 0.8697 (tpm170) cc_final: 0.8356 (tpm170) REVERT: Y 673 TYR cc_start: 0.6535 (m-80) cc_final: 0.6312 (m-80) REVERT: Y 694 LYS cc_start: 0.7623 (mmmt) cc_final: 0.7146 (mmmt) REVERT: Y 762 ILE cc_start: 0.8166 (pt) cc_final: 0.7738 (pt) REVERT: Z 1 MET cc_start: 0.7864 (tmm) cc_final: 0.7558 (tmm) REVERT: Z 9 LEU cc_start: 0.8371 (tp) cc_final: 0.8035 (mt) REVERT: Z 11 THR cc_start: 0.8201 (m) cc_final: 0.7079 (m) REVERT: Z 14 TYR cc_start: 0.7601 (p90) cc_final: 0.6820 (p90) REVERT: Z 94 GLU cc_start: 0.7926 (mp0) cc_final: 0.7586 (mp0) REVERT: Z 199 MET cc_start: 0.8632 (mmp) cc_final: 0.8238 (mmp) REVERT: Z 215 LYS cc_start: 0.7870 (mppt) cc_final: 0.7070 (mmtt) REVERT: Z 219 TYR cc_start: 0.7288 (m-10) cc_final: 0.6951 (m-80) REVERT: Z 267 TYR cc_start: 0.7359 (m-80) cc_final: 0.6928 (m-80) REVERT: Z 464 ILE cc_start: 0.9080 (mp) cc_final: 0.8123 (mp) REVERT: Z 500 GLU cc_start: 0.8565 (pp20) cc_final: 0.8250 (pp20) REVERT: Z 527 MET cc_start: 0.7921 (ptm) cc_final: 0.7604 (ppp) REVERT: Z 530 MET cc_start: 0.9054 (tpt) cc_final: 0.8711 (tpp) REVERT: Z 549 MET cc_start: 0.7869 (ppp) cc_final: 0.7591 (ppp) REVERT: Z 617 ARG cc_start: 0.8118 (ptm160) cc_final: 0.7895 (ptm160) REVERT: Z 623 GLU cc_start: 0.9225 (OUTLIER) cc_final: 0.8219 (tp30) REVERT: Z 721 ILE cc_start: 0.7916 (mp) cc_final: 0.7304 (mp) outliers start: 3 outliers final: 0 residues processed: 443 average time/residue: 0.3623 time to fit residues: 231.4514 Evaluate side-chains 380 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 379 time to evaluate : 1.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 114 optimal weight: 6.9990 chunk 90 optimal weight: 0.7980 chunk 175 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 130 optimal weight: 0.0970 chunk 203 optimal weight: 4.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 180 GLN X 183 ASN ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 302 GLN ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 457 ASN Z 8 GLN Z 97 ASN ** Z 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 769 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 18116 Z= 0.256 Angle : 0.786 9.968 24626 Z= 0.412 Chirality : 0.050 0.204 2820 Planarity : 0.006 0.070 3186 Dihedral : 6.618 25.438 2447 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.57 % Favored : 87.17 % Rotamer: Outliers : 0.10 % Allowed : 6.68 % Favored : 93.22 % 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: -3.70 (0.16), residues: 2244 helix: -1.07 (0.20), residues: 564 sheet: -2.42 (0.22), residues: 494 loop : -3.26 (0.16), residues: 1186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Y 262 HIS 0.010 0.002 HIS Y 170 PHE 0.027 0.002 PHE Y 505 TYR 0.029 0.002 TYR X 219 ARG 0.004 0.001 ARG Z 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 431 time to evaluate : 1.913 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 10 LEU cc_start: 0.8521 (tt) cc_final: 0.8261 (tt) REVERT: X 24 GLU cc_start: 0.8735 (pt0) cc_final: 0.8494 (pt0) REVERT: X 75 ASN cc_start: 0.8178 (p0) cc_final: 0.7618 (p0) REVERT: X 219 TYR cc_start: 0.7997 (m-80) cc_final: 0.7674 (m-80) REVERT: X 222 ASN cc_start: 0.8361 (m-40) cc_final: 0.7951 (p0) REVERT: X 242 ASP cc_start: 0.8202 (t0) cc_final: 0.7925 (t0) REVERT: X 251 ASN cc_start: 0.7978 (m110) cc_final: 0.7693 (m110) REVERT: X 265 MET cc_start: 0.4081 (mpp) cc_final: 0.3683 (mpp) REVERT: X 369 ARG cc_start: 0.7825 (ppt170) cc_final: 0.7604 (ttp80) REVERT: X 375 LEU cc_start: 0.8222 (mm) cc_final: 0.7983 (mm) REVERT: X 527 MET cc_start: 0.7392 (mtm) cc_final: 0.6030 (mtm) REVERT: X 549 MET cc_start: 0.8685 (mpp) cc_final: 0.8405 (mmm) REVERT: X 550 LYS cc_start: 0.8610 (pttm) cc_final: 0.7995 (pttp) REVERT: X 552 PHE cc_start: 0.8395 (t80) cc_final: 0.7426 (t80) REVERT: X 620 ARG cc_start: 0.8872 (ptm-80) cc_final: 0.8414 (ptm-80) REVERT: X 623 GLU cc_start: 0.8067 (mp0) cc_final: 0.7725 (mm-30) REVERT: X 666 LYS cc_start: 0.8339 (ptmm) cc_final: 0.7864 (tptp) REVERT: X 738 LYS cc_start: 0.8539 (mmpt) cc_final: 0.8308 (mmmt) REVERT: X 755 PHE cc_start: 0.8041 (m-80) cc_final: 0.7413 (m-10) REVERT: X 772 MET cc_start: 0.8640 (mtm) cc_final: 0.7954 (mtm) REVERT: X 773 GLN cc_start: 0.8930 (pt0) cc_final: 0.8560 (pt0) REVERT: Y 69 TYR cc_start: 0.7190 (m-80) cc_final: 0.6893 (m-80) REVERT: Y 75 ASN cc_start: 0.8272 (p0) cc_final: 0.7839 (p0) REVERT: Y 116 ASN cc_start: 0.7945 (m-40) cc_final: 0.7462 (t0) REVERT: Y 128 LEU cc_start: 0.7135 (tt) cc_final: 0.6649 (pp) REVERT: Y 142 ASP cc_start: 0.6646 (t0) cc_final: 0.5979 (t0) REVERT: Y 151 SER cc_start: 0.6778 (p) cc_final: 0.6561 (p) REVERT: Y 159 LEU cc_start: 0.9376 (mp) cc_final: 0.9059 (tp) REVERT: Y 204 ASP cc_start: 0.7580 (m-30) cc_final: 0.7190 (m-30) REVERT: Y 246 TYR cc_start: 0.7188 (t80) cc_final: 0.6984 (t80) REVERT: Y 265 MET cc_start: 0.7334 (mmp) cc_final: 0.6989 (mmp) REVERT: Y 267 TYR cc_start: 0.6387 (m-10) cc_final: 0.5753 (m-10) REVERT: Y 338 VAL cc_start: 0.8374 (p) cc_final: 0.8081 (m) REVERT: Y 356 TRP cc_start: 0.6209 (m-10) cc_final: 0.5959 (m-90) REVERT: Y 371 LEU cc_start: 0.8040 (pt) cc_final: 0.7772 (pp) REVERT: Y 405 HIS cc_start: 0.7341 (p90) cc_final: 0.7022 (p90) REVERT: Y 422 ASN cc_start: 0.7831 (t0) cc_final: 0.7524 (t0) REVERT: Y 444 LEU cc_start: 0.8608 (tp) cc_final: 0.8140 (pp) REVERT: Y 512 ILE cc_start: 0.8306 (pt) cc_final: 0.8058 (pt) REVERT: Y 520 LEU cc_start: 0.8673 (tp) cc_final: 0.7881 (mt) REVERT: Y 530 MET cc_start: 0.7497 (tpt) cc_final: 0.6656 (tpt) REVERT: Y 564 LEU cc_start: 0.9085 (tt) cc_final: 0.8857 (pp) REVERT: Y 591 TRP cc_start: 0.7887 (m-90) cc_final: 0.7264 (m-90) REVERT: Y 617 ARG cc_start: 0.8724 (tpm170) cc_final: 0.8394 (tpm170) REVERT: Y 694 LYS cc_start: 0.7842 (mmmt) cc_final: 0.7499 (mmmt) REVERT: Y 762 ILE cc_start: 0.7812 (pt) cc_final: 0.7567 (pt) REVERT: Z 1 MET cc_start: 0.8041 (tmm) cc_final: 0.7704 (tmm) REVERT: Z 14 TYR cc_start: 0.7650 (p90) cc_final: 0.6876 (p90) REVERT: Z 215 LYS cc_start: 0.7651 (mppt) cc_final: 0.6975 (mmtt) REVERT: Z 219 TYR cc_start: 0.7639 (m-10) cc_final: 0.7256 (m-80) REVERT: Z 267 TYR cc_start: 0.7212 (m-80) cc_final: 0.6823 (m-80) REVERT: Z 321 ASN cc_start: 0.5074 (t0) cc_final: 0.4741 (t0) REVERT: Z 445 ASP cc_start: 0.7529 (t0) cc_final: 0.7325 (t0) REVERT: Z 464 ILE cc_start: 0.8760 (mp) cc_final: 0.8424 (mp) REVERT: Z 500 GLU cc_start: 0.8503 (pp20) cc_final: 0.8163 (pp20) REVERT: Z 501 LEU cc_start: 0.8501 (mt) cc_final: 0.8099 (mt) REVERT: Z 527 MET cc_start: 0.8199 (ptm) cc_final: 0.7786 (pmm) REVERT: Z 530 MET cc_start: 0.8986 (tpt) cc_final: 0.8586 (tpp) REVERT: Z 549 MET cc_start: 0.7883 (ppp) cc_final: 0.7564 (ppp) REVERT: Z 550 LYS cc_start: 0.8340 (mmpt) cc_final: 0.7813 (mttm) REVERT: Z 620 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7280 (ptp-170) REVERT: Z 623 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8107 (mm-30) REVERT: Z 624 MET cc_start: 0.7901 (ptp) cc_final: 0.7321 (ptp) REVERT: Z 666 LYS cc_start: 0.8696 (tptm) cc_final: 0.8458 (tptp) REVERT: Z 673 TYR cc_start: 0.7602 (m-10) cc_final: 0.6956 (m-10) REVERT: Z 721 ILE cc_start: 0.7890 (mp) cc_final: 0.7505 (mp) outliers start: 2 outliers final: 1 residues processed: 433 average time/residue: 0.3584 time to fit residues: 222.9725 Evaluate side-chains 365 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 364 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 203 optimal weight: 0.7980 chunk 220 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 163 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 97 ASN ** X 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN Y 135 GLN ** Y 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 376 ASN ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 506 ASN ** Y 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 364 ASN ** Z 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.125 18116 Z= 0.316 Angle : 0.813 10.489 24626 Z= 0.428 Chirality : 0.050 0.237 2820 Planarity : 0.007 0.088 3186 Dihedral : 6.785 27.318 2447 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 29.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.28 % Favored : 86.45 % Rotamer: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % 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: -3.76 (0.16), residues: 2244 helix: -1.09 (0.20), residues: 577 sheet: -2.55 (0.21), residues: 517 loop : -3.28 (0.17), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Y 262 HIS 0.016 0.003 HIS X 315 PHE 0.027 0.002 PHE Z 277 TYR 0.026 0.002 TYR X 301 ARG 0.009 0.001 ARG X 674 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 2.126 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 75 ASN cc_start: 0.8227 (p0) cc_final: 0.7639 (p0) REVERT: X 219 TYR cc_start: 0.8174 (m-80) cc_final: 0.7908 (m-80) REVERT: X 222 ASN cc_start: 0.8510 (m-40) cc_final: 0.8093 (p0) REVERT: X 242 ASP cc_start: 0.8269 (t0) cc_final: 0.8041 (t0) REVERT: X 251 ASN cc_start: 0.8306 (m110) cc_final: 0.7981 (m110) REVERT: X 265 MET cc_start: 0.4164 (mpp) cc_final: 0.3836 (mpp) REVERT: X 291 TRP cc_start: 0.7618 (m-10) cc_final: 0.7100 (m-10) REVERT: X 303 TYR cc_start: 0.6499 (m-10) cc_final: 0.6279 (m-80) REVERT: X 404 LEU cc_start: 0.8299 (mp) cc_final: 0.7874 (pp) REVERT: X 491 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7234 (mtt180) REVERT: X 527 MET cc_start: 0.7610 (mtm) cc_final: 0.6520 (mtm) REVERT: X 549 MET cc_start: 0.8930 (mpp) cc_final: 0.8610 (mmm) REVERT: X 550 LYS cc_start: 0.8720 (pttm) cc_final: 0.8165 (pttp) REVERT: X 552 PHE cc_start: 0.8586 (t80) cc_final: 0.7617 (t80) REVERT: X 554 LYS cc_start: 0.9113 (tmtt) cc_final: 0.8880 (tptp) REVERT: X 617 ARG cc_start: 0.8593 (mmt-90) cc_final: 0.7690 (mpt180) REVERT: X 621 LEU cc_start: 0.9357 (pp) cc_final: 0.8797 (pp) REVERT: X 623 GLU cc_start: 0.8244 (mp0) cc_final: 0.7750 (mt-10) REVERT: X 666 LYS cc_start: 0.8540 (ptmm) cc_final: 0.7979 (tptp) REVERT: X 738 LYS cc_start: 0.8530 (mmpt) cc_final: 0.8269 (mmmt) REVERT: X 772 MET cc_start: 0.8731 (mtm) cc_final: 0.8048 (mtm) REVERT: X 773 GLN cc_start: 0.8883 (pt0) cc_final: 0.8493 (pt0) REVERT: Y 75 ASN cc_start: 0.8292 (p0) cc_final: 0.7860 (p0) REVERT: Y 94 GLU cc_start: 0.7940 (tt0) cc_final: 0.6696 (tm-30) REVERT: Y 116 ASN cc_start: 0.7946 (m-40) cc_final: 0.7334 (t0) REVERT: Y 128 LEU cc_start: 0.7250 (tt) cc_final: 0.6669 (pp) REVERT: Y 142 ASP cc_start: 0.6751 (t0) cc_final: 0.6115 (t0) REVERT: Y 151 SER cc_start: 0.6893 (p) cc_final: 0.6650 (p) REVERT: Y 159 LEU cc_start: 0.9371 (mp) cc_final: 0.9133 (tp) REVERT: Y 170 HIS cc_start: 0.8020 (t70) cc_final: 0.7674 (t70) REVERT: Y 213 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7069 (mm-30) REVERT: Y 216 CYS cc_start: 0.8913 (t) cc_final: 0.8554 (t) REVERT: Y 263 LYS cc_start: 0.7509 (mmmt) cc_final: 0.7228 (tppt) REVERT: Y 265 MET cc_start: 0.7159 (mmp) cc_final: 0.6353 (mmm) REVERT: Y 337 PHE cc_start: 0.7658 (m-80) cc_final: 0.7451 (m-10) REVERT: Y 356 TRP cc_start: 0.6512 (m-10) cc_final: 0.6236 (m-90) REVERT: Y 371 LEU cc_start: 0.8164 (pt) cc_final: 0.7904 (pp) REVERT: Y 405 HIS cc_start: 0.7240 (p90) cc_final: 0.7006 (p90) REVERT: Y 422 ASN cc_start: 0.7976 (t0) cc_final: 0.7496 (t0) REVERT: Y 444 LEU cc_start: 0.8714 (tp) cc_final: 0.8276 (pp) REVERT: Y 491 ARG cc_start: 0.8402 (mmp-170) cc_final: 0.8200 (mmp-170) REVERT: Y 530 MET cc_start: 0.7694 (tpt) cc_final: 0.6889 (tpt) REVERT: Y 546 THR cc_start: 0.8533 (p) cc_final: 0.8308 (p) REVERT: Y 591 TRP cc_start: 0.8095 (m-90) cc_final: 0.7222 (m-90) REVERT: Y 617 ARG cc_start: 0.8764 (tpm170) cc_final: 0.8449 (tpm170) REVERT: Y 649 THR cc_start: 0.7165 (p) cc_final: 0.6831 (p) REVERT: Y 694 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7693 (mmpt) REVERT: Y 729 ASN cc_start: 0.8380 (t0) cc_final: 0.8071 (t0) REVERT: Y 762 ILE cc_start: 0.8179 (pt) cc_final: 0.7735 (pt) REVERT: Z 11 THR cc_start: 0.8352 (m) cc_final: 0.7495 (m) REVERT: Z 14 TYR cc_start: 0.7859 (p90) cc_final: 0.7046 (p90) REVERT: Z 189 TYR cc_start: 0.8760 (m-80) cc_final: 0.8228 (m-10) REVERT: Z 219 TYR cc_start: 0.7987 (m-10) cc_final: 0.7447 (m-80) REVERT: Z 267 TYR cc_start: 0.7427 (m-80) cc_final: 0.7016 (m-80) REVERT: Z 352 TYR cc_start: 0.7936 (m-10) cc_final: 0.7671 (m-10) REVERT: Z 428 PHE cc_start: 0.7837 (m-10) cc_final: 0.7191 (m-80) REVERT: Z 527 MET cc_start: 0.8278 (ptm) cc_final: 0.7982 (pmm) REVERT: Z 530 MET cc_start: 0.8899 (tpt) cc_final: 0.8519 (tpp) REVERT: Z 549 MET cc_start: 0.8084 (ppp) cc_final: 0.7861 (ppp) REVERT: Z 552 PHE cc_start: 0.7768 (m-80) cc_final: 0.7562 (m-80) REVERT: Z 617 ARG cc_start: 0.8303 (ptm160) cc_final: 0.7794 (ptm160) REVERT: Z 623 GLU cc_start: 0.8833 (mm-30) cc_final: 0.7834 (mm-30) REVERT: Z 624 MET cc_start: 0.8184 (ptp) cc_final: 0.7547 (ptp) REVERT: Z 666 LYS cc_start: 0.8746 (tptm) cc_final: 0.8502 (tptp) REVERT: Z 673 TYR cc_start: 0.7544 (m-10) cc_final: 0.6792 (m-80) REVERT: Z 721 ILE cc_start: 0.7965 (mp) cc_final: 0.7554 (mp) REVERT: Z 768 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7828 (pt0) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.3465 time to fit residues: 201.8173 Evaluate side-chains 359 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 359 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 204 optimal weight: 0.0980 chunk 216 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 193 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 249 GLN ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 315 HIS ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN ** Y 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 457 ASN ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 773 GLN Z 611 GLN Z 677 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18116 Z= 0.212 Angle : 0.770 10.705 24626 Z= 0.395 Chirality : 0.050 0.217 2820 Planarity : 0.006 0.082 3186 Dihedral : 6.462 28.049 2447 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 22.28 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.50 % Favored : 88.24 % Rotamer: Outliers : 0.05 % Allowed : 5.08 % Favored : 94.87 % 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: -3.57 (0.16), residues: 2244 helix: -0.91 (0.21), residues: 560 sheet: -2.38 (0.22), residues: 485 loop : -3.18 (0.16), residues: 1199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP Y 262 HIS 0.014 0.002 HIS X 315 PHE 0.029 0.002 PHE Z 428 TYR 0.042 0.002 TYR X 448 ARG 0.011 0.001 ARG X 620 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 2.008 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 10 LEU cc_start: 0.8562 (tt) cc_final: 0.8293 (tt) REVERT: X 18 LEU cc_start: 0.8318 (mt) cc_final: 0.8087 (mt) REVERT: X 74 PHE cc_start: 0.8769 (t80) cc_final: 0.8477 (t80) REVERT: X 75 ASN cc_start: 0.8235 (p0) cc_final: 0.7634 (p0) REVERT: X 138 TRP cc_start: 0.7571 (m100) cc_final: 0.6859 (m100) REVERT: X 199 MET cc_start: 0.7510 (ppp) cc_final: 0.7107 (ppp) REVERT: X 219 TYR cc_start: 0.7893 (m-80) cc_final: 0.7661 (m-80) REVERT: X 222 ASN cc_start: 0.8326 (m-40) cc_final: 0.7898 (p0) REVERT: X 249 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8617 (pp30) REVERT: X 251 ASN cc_start: 0.7841 (m110) cc_final: 0.7523 (m110) REVERT: X 347 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8416 (mt-10) REVERT: X 404 LEU cc_start: 0.7909 (mp) cc_final: 0.7571 (pp) REVERT: X 491 ARG cc_start: 0.7476 (mtt180) cc_final: 0.7042 (mtt-85) REVERT: X 527 MET cc_start: 0.7531 (mtm) cc_final: 0.6967 (mtm) REVERT: X 531 PHE cc_start: 0.8204 (m-80) cc_final: 0.7760 (m-80) REVERT: X 549 MET cc_start: 0.8788 (mpp) cc_final: 0.8514 (mmm) REVERT: X 550 LYS cc_start: 0.8668 (pttm) cc_final: 0.8167 (pttp) REVERT: X 552 PHE cc_start: 0.8325 (t80) cc_final: 0.7356 (t80) REVERT: X 554 LYS cc_start: 0.9086 (tmtt) cc_final: 0.8786 (tptp) REVERT: X 662 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8299 (pt0) REVERT: X 666 LYS cc_start: 0.8376 (ptmm) cc_final: 0.7932 (tptp) REVERT: X 738 LYS cc_start: 0.8567 (mmpt) cc_final: 0.8224 (mmmt) REVERT: X 755 PHE cc_start: 0.8124 (m-80) cc_final: 0.7466 (m-10) REVERT: X 772 MET cc_start: 0.8559 (mtm) cc_final: 0.7787 (mtm) REVERT: X 773 GLN cc_start: 0.8753 (pt0) cc_final: 0.8331 (pt0) REVERT: Y 1 MET cc_start: 0.6928 (tpt) cc_final: 0.6209 (tpt) REVERT: Y 75 ASN cc_start: 0.8166 (p0) cc_final: 0.7715 (p0) REVERT: Y 94 GLU cc_start: 0.7802 (tt0) cc_final: 0.6564 (tm-30) REVERT: Y 116 ASN cc_start: 0.7793 (m-40) cc_final: 0.7281 (t0) REVERT: Y 128 LEU cc_start: 0.6964 (tt) cc_final: 0.6529 (pp) REVERT: Y 142 ASP cc_start: 0.6434 (t0) cc_final: 0.5867 (t0) REVERT: Y 151 SER cc_start: 0.6642 (p) cc_final: 0.6387 (p) REVERT: Y 159 LEU cc_start: 0.9319 (mp) cc_final: 0.9085 (tp) REVERT: Y 213 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7125 (mm-30) REVERT: Y 338 VAL cc_start: 0.8249 (p) cc_final: 0.8000 (m) REVERT: Y 371 LEU cc_start: 0.7943 (pt) cc_final: 0.7730 (pp) REVERT: Y 405 HIS cc_start: 0.7073 (p90) cc_final: 0.6859 (p90) REVERT: Y 444 LEU cc_start: 0.8650 (tp) cc_final: 0.8147 (pp) REVERT: Y 505 PHE cc_start: 0.8115 (m-80) cc_final: 0.7872 (m-80) REVERT: Y 530 MET cc_start: 0.7535 (tpt) cc_final: 0.6744 (tpt) REVERT: Y 547 ASN cc_start: 0.8504 (m-40) cc_final: 0.8300 (m-40) REVERT: Y 591 TRP cc_start: 0.7814 (m-90) cc_final: 0.7429 (m-90) REVERT: Y 617 ARG cc_start: 0.8737 (tpm170) cc_final: 0.8346 (tpm170) REVERT: Y 618 ARG cc_start: 0.8950 (mtp180) cc_final: 0.8678 (ttm170) REVERT: Y 693 TYR cc_start: 0.6106 (m-80) cc_final: 0.5436 (m-80) REVERT: Y 694 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7641 (mmmt) REVERT: Y 728 LYS cc_start: 0.6333 (tttt) cc_final: 0.5882 (mmtm) REVERT: Y 762 ILE cc_start: 0.7983 (pt) cc_final: 0.7557 (pt) REVERT: Z 9 LEU cc_start: 0.8377 (mt) cc_final: 0.8169 (mt) REVERT: Z 11 THR cc_start: 0.8232 (m) cc_final: 0.7680 (p) REVERT: Z 14 TYR cc_start: 0.7583 (p90) cc_final: 0.6794 (p90) REVERT: Z 82 MET cc_start: 0.5490 (mpp) cc_final: 0.5193 (mpp) REVERT: Z 189 TYR cc_start: 0.8609 (m-80) cc_final: 0.8051 (m-10) REVERT: Z 215 LYS cc_start: 0.7861 (mppt) cc_final: 0.7293 (mmtt) REVERT: Z 219 TYR cc_start: 0.7963 (m-10) cc_final: 0.7535 (m-80) REVERT: Z 265 MET cc_start: 0.7494 (mpp) cc_final: 0.6395 (mpp) REVERT: Z 267 TYR cc_start: 0.7366 (m-80) cc_final: 0.7113 (m-80) REVERT: Z 321 ASN cc_start: 0.4229 (t0) cc_final: 0.3946 (t0) REVERT: Z 352 TYR cc_start: 0.7383 (m-80) cc_final: 0.7117 (m-80) REVERT: Z 428 PHE cc_start: 0.8035 (m-10) cc_final: 0.7448 (m-80) REVERT: Z 445 ASP cc_start: 0.7236 (t0) cc_final: 0.6976 (t0) REVERT: Z 477 ASN cc_start: 0.8312 (t0) cc_final: 0.8015 (t0) REVERT: Z 479 ASP cc_start: 0.8571 (m-30) cc_final: 0.7685 (m-30) REVERT: Z 500 GLU cc_start: 0.8420 (pp20) cc_final: 0.8187 (pp20) REVERT: Z 501 LEU cc_start: 0.8518 (mt) cc_final: 0.8314 (mt) REVERT: Z 514 MET cc_start: 0.6909 (tmm) cc_final: 0.6629 (tmm) REVERT: Z 527 MET cc_start: 0.8253 (ptm) cc_final: 0.8021 (pmm) REVERT: Z 530 MET cc_start: 0.8888 (tpt) cc_final: 0.8458 (tpp) REVERT: Z 549 MET cc_start: 0.8079 (ppp) cc_final: 0.7554 (ppp) REVERT: Z 550 LYS cc_start: 0.8611 (tmtt) cc_final: 0.8245 (tptp) REVERT: Z 617 ARG cc_start: 0.8245 (ptm160) cc_final: 0.7810 (ptm160) REVERT: Z 620 ARG cc_start: 0.8149 (mtp180) cc_final: 0.7319 (ptp-170) REVERT: Z 623 GLU cc_start: 0.8803 (mm-30) cc_final: 0.7699 (mm-30) REVERT: Z 624 MET cc_start: 0.8113 (ptp) cc_final: 0.7580 (ptp) REVERT: Z 666 LYS cc_start: 0.8710 (tptm) cc_final: 0.8470 (tptp) REVERT: Z 673 TYR cc_start: 0.7405 (m-10) cc_final: 0.6537 (m-10) REVERT: Z 721 ILE cc_start: 0.7879 (mp) cc_final: 0.7302 (mp) outliers start: 1 outliers final: 0 residues processed: 399 average time/residue: 0.3666 time to fit residues: 213.8456 Evaluate side-chains 354 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.8980 chunk 122 optimal weight: 0.2980 chunk 3 optimal weight: 5.9990 chunk 161 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 149 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 194 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 315 HIS ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN Y 492 GLN ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6753 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 18116 Z= 0.242 Angle : 0.765 10.698 24626 Z= 0.395 Chirality : 0.049 0.186 2820 Planarity : 0.006 0.132 3186 Dihedral : 6.437 29.594 2447 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.75 % Favored : 86.99 % Rotamer: Outliers : 0.05 % Allowed : 4.09 % Favored : 95.86 % 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: -3.55 (0.16), residues: 2244 helix: -0.88 (0.21), residues: 568 sheet: -2.43 (0.21), residues: 499 loop : -3.16 (0.17), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP Y 262 HIS 0.013 0.002 HIS X 315 PHE 0.036 0.002 PHE Z 140 TYR 0.034 0.002 TYR X 448 ARG 0.009 0.001 ARG Y 429 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 401 time to evaluate : 1.859 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 10 LEU cc_start: 0.8711 (tt) cc_final: 0.8430 (tt) REVERT: X 18 LEU cc_start: 0.8368 (mt) cc_final: 0.8129 (mt) REVERT: X 74 PHE cc_start: 0.8744 (t80) cc_final: 0.8485 (t80) REVERT: X 75 ASN cc_start: 0.8049 (p0) cc_final: 0.7365 (p0) REVERT: X 138 TRP cc_start: 0.7711 (m100) cc_final: 0.7010 (m100) REVERT: X 199 MET cc_start: 0.7586 (ppp) cc_final: 0.7127 (ppp) REVERT: X 219 TYR cc_start: 0.8091 (m-80) cc_final: 0.7733 (m-80) REVERT: X 222 ASN cc_start: 0.8457 (m-40) cc_final: 0.8033 (p0) REVERT: X 291 TRP cc_start: 0.7467 (m-10) cc_final: 0.6895 (m-10) REVERT: X 347 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8230 (mm-30) REVERT: X 491 ARG cc_start: 0.7446 (mtt180) cc_final: 0.7027 (mtt-85) REVERT: X 527 MET cc_start: 0.7615 (mtm) cc_final: 0.7100 (mtm) REVERT: X 531 PHE cc_start: 0.8249 (m-80) cc_final: 0.7847 (m-80) REVERT: X 544 MET cc_start: 0.7922 (mmp) cc_final: 0.7678 (mmp) REVERT: X 549 MET cc_start: 0.8860 (mpp) cc_final: 0.8583 (mmm) REVERT: X 552 PHE cc_start: 0.8386 (t80) cc_final: 0.7450 (t80) REVERT: X 554 LYS cc_start: 0.9115 (tmtt) cc_final: 0.8846 (tptp) REVERT: X 617 ARG cc_start: 0.8411 (mmt-90) cc_final: 0.7937 (mpt180) REVERT: X 623 GLU cc_start: 0.8017 (mp0) cc_final: 0.7562 (mm-30) REVERT: X 662 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8442 (pt0) REVERT: X 727 LEU cc_start: 0.8602 (mm) cc_final: 0.8286 (mt) REVERT: X 738 LYS cc_start: 0.8618 (mmpt) cc_final: 0.8336 (mmmt) REVERT: X 772 MET cc_start: 0.8595 (mtm) cc_final: 0.7952 (mtm) REVERT: Y 1 MET cc_start: 0.7325 (tpt) cc_final: 0.6788 (tpt) REVERT: Y 75 ASN cc_start: 0.8217 (p0) cc_final: 0.7866 (p0) REVERT: Y 94 GLU cc_start: 0.7882 (tt0) cc_final: 0.6638 (tm-30) REVERT: Y 101 ARG cc_start: 0.7768 (mpt180) cc_final: 0.6562 (mpt180) REVERT: Y 116 ASN cc_start: 0.7799 (m-40) cc_final: 0.7174 (t0) REVERT: Y 128 LEU cc_start: 0.7129 (tt) cc_final: 0.6645 (pp) REVERT: Y 142 ASP cc_start: 0.6568 (t0) cc_final: 0.6042 (t0) REVERT: Y 151 SER cc_start: 0.6822 (p) cc_final: 0.6557 (p) REVERT: Y 159 LEU cc_start: 0.9271 (mp) cc_final: 0.9024 (tp) REVERT: Y 170 HIS cc_start: 0.7962 (t70) cc_final: 0.7660 (t70) REVERT: Y 208 ILE cc_start: 0.8714 (mm) cc_final: 0.8499 (mm) REVERT: Y 213 GLU cc_start: 0.7560 (mt-10) cc_final: 0.6912 (mm-30) REVERT: Y 246 TYR cc_start: 0.6972 (t80) cc_final: 0.6760 (t80) REVERT: Y 338 VAL cc_start: 0.8197 (p) cc_final: 0.7937 (m) REVERT: Y 363 ARG cc_start: 0.7921 (ttt180) cc_final: 0.7349 (ttp-170) REVERT: Y 434 GLU cc_start: 0.8313 (pm20) cc_final: 0.8061 (mm-30) REVERT: Y 444 LEU cc_start: 0.8682 (tp) cc_final: 0.8196 (pp) REVERT: Y 505 PHE cc_start: 0.8147 (m-80) cc_final: 0.7873 (m-80) REVERT: Y 530 MET cc_start: 0.7518 (tpt) cc_final: 0.6805 (tpt) REVERT: Y 591 TRP cc_start: 0.8076 (m-90) cc_final: 0.7297 (m-90) REVERT: Y 617 ARG cc_start: 0.8780 (tpm170) cc_final: 0.8442 (tpm170) REVERT: Y 694 LYS cc_start: 0.7968 (mmmt) cc_final: 0.7640 (mmmt) REVERT: Y 707 LYS cc_start: 0.9162 (tttm) cc_final: 0.8906 (tttp) REVERT: Y 762 ILE cc_start: 0.8139 (pt) cc_final: 0.7771 (pt) REVERT: Z 11 THR cc_start: 0.8341 (m) cc_final: 0.7909 (p) REVERT: Z 14 TYR cc_start: 0.7659 (p90) cc_final: 0.6937 (p90) REVERT: Z 82 MET cc_start: 0.5754 (mpp) cc_final: 0.5442 (mpp) REVERT: Z 189 TYR cc_start: 0.8619 (m-80) cc_final: 0.7922 (m-10) REVERT: Z 199 MET cc_start: 0.8558 (mmp) cc_final: 0.8139 (tmm) REVERT: Z 215 LYS cc_start: 0.7896 (mppt) cc_final: 0.7361 (mmmt) REVERT: Z 219 TYR cc_start: 0.7958 (m-10) cc_final: 0.7504 (m-80) REVERT: Z 267 TYR cc_start: 0.7543 (m-80) cc_final: 0.7122 (m-80) REVERT: Z 346 LYS cc_start: 0.8173 (ptmm) cc_final: 0.7972 (ttpp) REVERT: Z 352 TYR cc_start: 0.7419 (m-80) cc_final: 0.7133 (m-80) REVERT: Z 374 ASN cc_start: 0.7513 (p0) cc_final: 0.7222 (p0) REVERT: Z 421 LEU cc_start: 0.8285 (mt) cc_final: 0.8082 (mt) REVERT: Z 428 PHE cc_start: 0.8074 (m-10) cc_final: 0.7191 (m-80) REVERT: Z 441 ARG cc_start: 0.7515 (ptt180) cc_final: 0.7208 (ptt180) REVERT: Z 479 ASP cc_start: 0.8644 (m-30) cc_final: 0.7663 (m-30) REVERT: Z 500 GLU cc_start: 0.8730 (pp20) cc_final: 0.8224 (pp20) REVERT: Z 501 LEU cc_start: 0.8616 (mt) cc_final: 0.8078 (mt) REVERT: Z 530 MET cc_start: 0.8825 (tpt) cc_final: 0.8389 (tpp) REVERT: Z 549 MET cc_start: 0.8279 (ppp) cc_final: 0.7211 (ppp) REVERT: Z 550 LYS cc_start: 0.8678 (tmtt) cc_final: 0.8430 (mmtp) REVERT: Z 551 LYS cc_start: 0.8034 (ptpt) cc_final: 0.7634 (ptpt) REVERT: Z 552 PHE cc_start: 0.8141 (m-10) cc_final: 0.7904 (m-10) REVERT: Z 617 ARG cc_start: 0.8242 (ptm160) cc_final: 0.7778 (ptm160) REVERT: Z 622 LYS cc_start: 0.8506 (mmpt) cc_final: 0.8241 (mmpt) REVERT: Z 623 GLU cc_start: 0.8869 (mm-30) cc_final: 0.7975 (mm-30) REVERT: Z 624 MET cc_start: 0.8125 (ptp) cc_final: 0.7595 (ptp) REVERT: Z 627 GLN cc_start: 0.7703 (pp30) cc_final: 0.7110 (pp30) REVERT: Z 666 LYS cc_start: 0.8709 (tptm) cc_final: 0.8481 (tptp) REVERT: Z 673 TYR cc_start: 0.7543 (m-10) cc_final: 0.6819 (m-10) REVERT: Z 721 ILE cc_start: 0.7993 (mp) cc_final: 0.7399 (mp) REVERT: Z 768 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7793 (pt0) outliers start: 1 outliers final: 1 residues processed: 402 average time/residue: 0.3472 time to fit residues: 201.2251 Evaluate side-chains 367 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 366 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 0.8980 chunk 194 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 216 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 113 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 188 HIS ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 315 HIS ** Y 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6658 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 18116 Z= 0.202 Angle : 0.763 10.818 24626 Z= 0.387 Chirality : 0.050 0.245 2820 Planarity : 0.006 0.077 3186 Dihedral : 6.206 30.745 2447 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.45 % Favored : 88.28 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.17), residues: 2244 helix: -0.86 (0.21), residues: 572 sheet: -2.47 (0.21), residues: 487 loop : -3.08 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP Y 262 HIS 0.011 0.002 HIS X 315 PHE 0.035 0.002 PHE Z 140 TYR 0.037 0.002 TYR X 448 ARG 0.008 0.000 ARG X 674 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.843 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 10 LEU cc_start: 0.8613 (tt) cc_final: 0.8303 (tt) REVERT: X 74 PHE cc_start: 0.8769 (t80) cc_final: 0.8447 (t80) REVERT: X 75 ASN cc_start: 0.7998 (p0) cc_final: 0.7425 (p0) REVERT: X 138 TRP cc_start: 0.7368 (m100) cc_final: 0.6750 (m100) REVERT: X 199 MET cc_start: 0.7373 (ppp) cc_final: 0.7036 (ppp) REVERT: X 215 LYS cc_start: 0.7914 (mppt) cc_final: 0.7642 (mmtm) REVERT: X 219 TYR cc_start: 0.8005 (m-80) cc_final: 0.7650 (m-80) REVERT: X 222 ASN cc_start: 0.8328 (m-40) cc_final: 0.7910 (p0) REVERT: X 291 TRP cc_start: 0.7402 (m-10) cc_final: 0.6975 (m-10) REVERT: X 317 THR cc_start: 0.5158 (m) cc_final: 0.4627 (m) REVERT: X 347 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8232 (mt-10) REVERT: X 375 LEU cc_start: 0.8142 (mm) cc_final: 0.7917 (mm) REVERT: X 429 ARG cc_start: 0.8555 (ppt170) cc_final: 0.8218 (ppt170) REVERT: X 491 ARG cc_start: 0.7442 (mtt180) cc_final: 0.7083 (mtt-85) REVERT: X 527 MET cc_start: 0.7650 (mtm) cc_final: 0.6261 (mtm) REVERT: X 544 MET cc_start: 0.7910 (mmp) cc_final: 0.7596 (mmp) REVERT: X 549 MET cc_start: 0.8705 (mpp) cc_final: 0.8399 (mmt) REVERT: X 552 PHE cc_start: 0.8189 (t80) cc_final: 0.7318 (t80) REVERT: X 554 LYS cc_start: 0.9015 (tmtt) cc_final: 0.8747 (tptp) REVERT: X 617 ARG cc_start: 0.8499 (mmt-90) cc_final: 0.7849 (mpt180) REVERT: X 623 GLU cc_start: 0.7802 (mp0) cc_final: 0.7425 (mm-30) REVERT: X 662 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8342 (pt0) REVERT: X 738 LYS cc_start: 0.8578 (mmpt) cc_final: 0.8257 (mmmt) REVERT: X 772 MET cc_start: 0.8561 (mtm) cc_final: 0.7908 (mtm) REVERT: Y 1 MET cc_start: 0.7022 (tpt) cc_final: 0.6431 (tpt) REVERT: Y 64 LEU cc_start: 0.9208 (pp) cc_final: 0.8798 (pp) REVERT: Y 94 GLU cc_start: 0.7813 (tt0) cc_final: 0.6591 (tm-30) REVERT: Y 101 ARG cc_start: 0.7551 (mpt180) cc_final: 0.6385 (mpt180) REVERT: Y 116 ASN cc_start: 0.7819 (m-40) cc_final: 0.7301 (t0) REVERT: Y 128 LEU cc_start: 0.6953 (tt) cc_final: 0.6572 (pp) REVERT: Y 142 ASP cc_start: 0.6414 (t0) cc_final: 0.5981 (t0) REVERT: Y 151 SER cc_start: 0.6903 (p) cc_final: 0.6659 (p) REVERT: Y 159 LEU cc_start: 0.9277 (mp) cc_final: 0.9045 (tp) REVERT: Y 204 ASP cc_start: 0.7373 (m-30) cc_final: 0.7104 (m-30) REVERT: Y 213 GLU cc_start: 0.7710 (mt-10) cc_final: 0.6843 (mm-30) REVERT: Y 338 VAL cc_start: 0.8135 (p) cc_final: 0.7893 (m) REVERT: Y 346 LYS cc_start: 0.8627 (ptpp) cc_final: 0.8338 (ptmm) REVERT: Y 443 ARG cc_start: 0.8069 (mmp-170) cc_final: 0.7520 (mmp80) REVERT: Y 444 LEU cc_start: 0.8642 (tp) cc_final: 0.8132 (pp) REVERT: Y 505 PHE cc_start: 0.8172 (m-10) cc_final: 0.7950 (m-80) REVERT: Y 530 MET cc_start: 0.7471 (tpt) cc_final: 0.6757 (tpt) REVERT: Y 591 TRP cc_start: 0.7902 (m-90) cc_final: 0.7133 (m-90) REVERT: Y 617 ARG cc_start: 0.8755 (tpm170) cc_final: 0.8373 (tpm170) REVERT: Y 694 LYS cc_start: 0.7950 (mmmt) cc_final: 0.7538 (mmmt) REVERT: Y 744 LEU cc_start: 0.9027 (mt) cc_final: 0.8647 (pp) REVERT: Z 11 THR cc_start: 0.8300 (m) cc_final: 0.7711 (p) REVERT: Z 14 TYR cc_start: 0.7536 (p90) cc_final: 0.6729 (p90) REVERT: Z 82 MET cc_start: 0.5746 (mpp) cc_final: 0.5176 (mpp) REVERT: Z 189 TYR cc_start: 0.8565 (m-80) cc_final: 0.7835 (m-10) REVERT: Z 215 LYS cc_start: 0.7896 (mppt) cc_final: 0.7232 (mmtp) REVERT: Z 219 TYR cc_start: 0.7943 (m-10) cc_final: 0.7489 (m-80) REVERT: Z 267 TYR cc_start: 0.7435 (m-80) cc_final: 0.7110 (m-80) REVERT: Z 346 LYS cc_start: 0.8031 (ptmm) cc_final: 0.7791 (ttpp) REVERT: Z 352 TYR cc_start: 0.7346 (m-80) cc_final: 0.7070 (m-10) REVERT: Z 374 ASN cc_start: 0.7400 (p0) cc_final: 0.7036 (p0) REVERT: Z 421 LEU cc_start: 0.7965 (mt) cc_final: 0.7748 (mt) REVERT: Z 428 PHE cc_start: 0.7949 (m-10) cc_final: 0.7300 (m-80) REVERT: Z 441 ARG cc_start: 0.7459 (ptt180) cc_final: 0.7172 (ptt180) REVERT: Z 500 GLU cc_start: 0.8610 (pp20) cc_final: 0.8066 (pp20) REVERT: Z 501 LEU cc_start: 0.8583 (mt) cc_final: 0.8216 (mt) REVERT: Z 514 MET cc_start: 0.6839 (tmm) cc_final: 0.6511 (tmm) REVERT: Z 530 MET cc_start: 0.8721 (tpt) cc_final: 0.8268 (tpp) REVERT: Z 549 MET cc_start: 0.8083 (ppp) cc_final: 0.7539 (ppp) REVERT: Z 550 LYS cc_start: 0.8643 (tmtt) cc_final: 0.8333 (tptp) REVERT: Z 551 LYS cc_start: 0.7993 (ptpt) cc_final: 0.7693 (ptpt) REVERT: Z 617 ARG cc_start: 0.8218 (ptm160) cc_final: 0.7759 (ptm160) REVERT: Z 622 LYS cc_start: 0.8467 (mmpt) cc_final: 0.8117 (mmpt) REVERT: Z 623 GLU cc_start: 0.8881 (mm-30) cc_final: 0.7843 (mm-30) REVERT: Z 624 MET cc_start: 0.8081 (ptp) cc_final: 0.7491 (ptp) REVERT: Z 629 GLU cc_start: 0.7691 (mp0) cc_final: 0.7367 (mp0) REVERT: Z 666 LYS cc_start: 0.8692 (tptm) cc_final: 0.8464 (tptp) REVERT: Z 673 TYR cc_start: 0.7353 (m-10) cc_final: 0.6765 (m-10) REVERT: Z 721 ILE cc_start: 0.7955 (mp) cc_final: 0.7353 (mp) REVERT: Z 768 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7741 (pt0) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.3596 time to fit residues: 214.6480 Evaluate side-chains 362 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 362 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 158 optimal weight: 30.0000 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 135 optimal weight: 0.0070 chunk 131 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 422 ASN ** X 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 740 GLN Y 97 ASN ** Y 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 632 ASN ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 279 ASN Z 739 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6778 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 18116 Z= 0.250 Angle : 0.779 11.609 24626 Z= 0.400 Chirality : 0.050 0.225 2820 Planarity : 0.006 0.083 3186 Dihedral : 6.330 41.657 2447 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 25.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.52 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.16), residues: 2244 helix: -0.90 (0.21), residues: 567 sheet: -2.52 (0.21), residues: 503 loop : -3.10 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP Y 262 HIS 0.007 0.002 HIS X 245 PHE 0.030 0.002 PHE Z 140 TYR 0.026 0.002 TYR X 448 ARG 0.008 0.001 ARG X 674 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 2.049 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 10 LEU cc_start: 0.8640 (tt) cc_final: 0.8351 (tt) REVERT: X 18 LEU cc_start: 0.8333 (mt) cc_final: 0.8043 (mt) REVERT: X 40 PHE cc_start: 0.7206 (p90) cc_final: 0.6738 (p90) REVERT: X 74 PHE cc_start: 0.8726 (t80) cc_final: 0.8481 (t80) REVERT: X 75 ASN cc_start: 0.8038 (p0) cc_final: 0.7378 (p0) REVERT: X 108 ILE cc_start: 0.7161 (mp) cc_final: 0.6909 (mp) REVERT: X 138 TRP cc_start: 0.7677 (m100) cc_final: 0.6739 (m100) REVERT: X 199 MET cc_start: 0.7502 (ppp) cc_final: 0.7073 (ppp) REVERT: X 219 TYR cc_start: 0.8115 (m-80) cc_final: 0.7720 (m-80) REVERT: X 222 ASN cc_start: 0.8458 (m-40) cc_final: 0.8038 (p0) REVERT: X 265 MET cc_start: 0.3642 (mpp) cc_final: 0.3428 (mpp) REVERT: X 291 TRP cc_start: 0.7517 (m-10) cc_final: 0.7121 (m-10) REVERT: X 296 PHE cc_start: 0.7272 (m-80) cc_final: 0.6996 (m-10) REVERT: X 317 THR cc_start: 0.5777 (m) cc_final: 0.5389 (m) REVERT: X 347 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8264 (mt-10) REVERT: X 376 ASN cc_start: 0.7633 (t0) cc_final: 0.7107 (t0) REVERT: X 404 LEU cc_start: 0.7776 (mp) cc_final: 0.7468 (pp) REVERT: X 491 ARG cc_start: 0.7507 (mtt180) cc_final: 0.7153 (mtt-85) REVERT: X 527 MET cc_start: 0.7819 (mtm) cc_final: 0.6391 (mtm) REVERT: X 544 MET cc_start: 0.7778 (mmp) cc_final: 0.7272 (mmp) REVERT: X 549 MET cc_start: 0.8777 (mpp) cc_final: 0.8500 (mmt) REVERT: X 552 PHE cc_start: 0.8412 (t80) cc_final: 0.7543 (t80) REVERT: X 554 LYS cc_start: 0.9098 (tmtt) cc_final: 0.8819 (tptp) REVERT: X 623 GLU cc_start: 0.7989 (mp0) cc_final: 0.7539 (mm-30) REVERT: X 662 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8472 (pt0) REVERT: X 727 LEU cc_start: 0.8528 (mm) cc_final: 0.8322 (mm) REVERT: X 738 LYS cc_start: 0.8629 (mmpt) cc_final: 0.8340 (mmmt) REVERT: X 748 ASP cc_start: 0.9073 (t0) cc_final: 0.8844 (t0) REVERT: X 772 MET cc_start: 0.8614 (mtm) cc_final: 0.7942 (mtm) REVERT: Y 1 MET cc_start: 0.7187 (tpt) cc_final: 0.6625 (tpt) REVERT: Y 94 GLU cc_start: 0.7948 (tt0) cc_final: 0.6748 (tm-30) REVERT: Y 101 ARG cc_start: 0.7882 (mpt180) cc_final: 0.7476 (mmm160) REVERT: Y 107 LEU cc_start: 0.8154 (tp) cc_final: 0.7911 (mm) REVERT: Y 116 ASN cc_start: 0.7808 (m-40) cc_final: 0.7187 (t0) REVERT: Y 128 LEU cc_start: 0.7182 (tt) cc_final: 0.6705 (pp) REVERT: Y 142 ASP cc_start: 0.6613 (t0) cc_final: 0.6121 (t0) REVERT: Y 159 LEU cc_start: 0.9278 (mp) cc_final: 0.9055 (tp) REVERT: Y 204 ASP cc_start: 0.7785 (m-30) cc_final: 0.7538 (m-30) REVERT: Y 208 ILE cc_start: 0.8709 (tt) cc_final: 0.8488 (mm) REVERT: Y 213 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7034 (mm-30) REVERT: Y 338 VAL cc_start: 0.8157 (p) cc_final: 0.7868 (m) REVERT: Y 346 LYS cc_start: 0.8680 (ptpp) cc_final: 0.8401 (ptmm) REVERT: Y 363 ARG cc_start: 0.7989 (ttt180) cc_final: 0.7307 (ttp-170) REVERT: Y 444 LEU cc_start: 0.8687 (tp) cc_final: 0.8238 (pp) REVERT: Y 505 PHE cc_start: 0.8211 (m-10) cc_final: 0.7966 (m-80) REVERT: Y 527 MET cc_start: 0.8517 (mmt) cc_final: 0.8266 (mmm) REVERT: Y 547 ASN cc_start: 0.8439 (m-40) cc_final: 0.8236 (m-40) REVERT: Y 552 PHE cc_start: 0.7022 (t80) cc_final: 0.6485 (t80) REVERT: Y 591 TRP cc_start: 0.8052 (m-90) cc_final: 0.7088 (m-90) REVERT: Y 617 ARG cc_start: 0.8794 (tpm170) cc_final: 0.8403 (tpm170) REVERT: Y 694 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7634 (mmmt) REVERT: Y 729 ASN cc_start: 0.8344 (t0) cc_final: 0.8088 (t0) REVERT: Y 762 ILE cc_start: 0.8083 (pt) cc_final: 0.7668 (pt) REVERT: Z 11 THR cc_start: 0.8443 (m) cc_final: 0.7841 (m) REVERT: Z 14 TYR cc_start: 0.7720 (p90) cc_final: 0.6901 (p90) REVERT: Z 189 TYR cc_start: 0.8632 (m-80) cc_final: 0.7898 (m-10) REVERT: Z 199 MET cc_start: 0.8554 (mmp) cc_final: 0.8346 (tpp) REVERT: Z 219 TYR cc_start: 0.7939 (m-10) cc_final: 0.7368 (m-80) REVERT: Z 267 TYR cc_start: 0.7642 (m-80) cc_final: 0.7264 (m-80) REVERT: Z 338 VAL cc_start: 0.7250 (t) cc_final: 0.7000 (p) REVERT: Z 352 TYR cc_start: 0.7378 (m-80) cc_final: 0.7075 (m-80) REVERT: Z 356 TRP cc_start: 0.5597 (m100) cc_final: 0.5007 (m100) REVERT: Z 374 ASN cc_start: 0.7608 (p0) cc_final: 0.7275 (p0) REVERT: Z 428 PHE cc_start: 0.8060 (m-10) cc_final: 0.7178 (m-80) REVERT: Z 441 ARG cc_start: 0.7478 (ptt180) cc_final: 0.7070 (ptt180) REVERT: Z 500 GLU cc_start: 0.8705 (pp20) cc_final: 0.8156 (pp20) REVERT: Z 501 LEU cc_start: 0.8646 (mt) cc_final: 0.8258 (mt) REVERT: Z 514 MET cc_start: 0.7093 (tmm) cc_final: 0.6830 (tmm) REVERT: Z 530 MET cc_start: 0.8760 (tpt) cc_final: 0.8277 (tpp) REVERT: Z 549 MET cc_start: 0.8144 (ppp) cc_final: 0.7749 (ppp) REVERT: Z 550 LYS cc_start: 0.8669 (tmtt) cc_final: 0.8351 (tptp) REVERT: Z 551 LYS cc_start: 0.8086 (ptpt) cc_final: 0.7741 (ptpt) REVERT: Z 591 TRP cc_start: 0.7323 (m-10) cc_final: 0.7102 (m-10) REVERT: Z 617 ARG cc_start: 0.8211 (ptm160) cc_final: 0.7785 (ptm160) REVERT: Z 622 LYS cc_start: 0.8564 (mmpt) cc_final: 0.8243 (mmpt) REVERT: Z 623 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8077 (mm-30) REVERT: Z 624 MET cc_start: 0.8138 (ptp) cc_final: 0.7625 (ptp) REVERT: Z 627 GLN cc_start: 0.7719 (pp30) cc_final: 0.7148 (pp30) REVERT: Z 629 GLU cc_start: 0.7811 (mp0) cc_final: 0.7324 (mp0) REVERT: Z 666 LYS cc_start: 0.8787 (tptm) cc_final: 0.8533 (tptp) REVERT: Z 673 TYR cc_start: 0.7488 (m-10) cc_final: 0.6992 (m-10) REVERT: Z 721 ILE cc_start: 0.8026 (mp) cc_final: 0.7551 (mp) REVERT: Z 768 GLU cc_start: 0.7978 (mt-10) cc_final: 0.7769 (pt0) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.3423 time to fit residues: 203.5430 Evaluate side-chains 371 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 371 time to evaluate : 2.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 128 optimal weight: 0.0070 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 106 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 188 HIS ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 315 HIS ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 436 HIS Y 506 ASN ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18116 Z= 0.202 Angle : 0.769 10.779 24626 Z= 0.389 Chirality : 0.050 0.213 2820 Planarity : 0.006 0.080 3186 Dihedral : 6.085 32.891 2447 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.19 % Favored : 88.55 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.17), residues: 2244 helix: -0.80 (0.21), residues: 561 sheet: -2.35 (0.22), residues: 479 loop : -3.01 (0.17), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP Y 262 HIS 0.010 0.002 HIS X 315 PHE 0.030 0.002 PHE Z 140 TYR 0.031 0.002 TYR Y 462 ARG 0.011 0.001 ARG Z 307 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 2.157 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: symmetry clash revert: 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 18 LEU cc_start: 0.8394 (mt) cc_final: 0.8119 (mt) REVERT: X 40 PHE cc_start: 0.7134 (p90) cc_final: 0.6611 (p90) REVERT: X 74 PHE cc_start: 0.8747 (t80) cc_final: 0.8412 (t80) REVERT: X 75 ASN cc_start: 0.7894 (p0) cc_final: 0.7323 (p0) REVERT: X 138 TRP cc_start: 0.7162 (m100) cc_final: 0.6619 (m100) REVERT: X 219 TYR cc_start: 0.7985 (m-80) cc_final: 0.7614 (m-80) REVERT: X 222 ASN cc_start: 0.8330 (m-40) cc_final: 0.7915 (p0) REVERT: X 296 PHE cc_start: 0.7127 (m-80) cc_final: 0.6875 (m-10) REVERT: X 317 THR cc_start: 0.5437 (m) cc_final: 0.5050 (m) REVERT: X 491 ARG cc_start: 0.7493 (mtt180) cc_final: 0.7184 (mtt-85) REVERT: X 527 MET cc_start: 0.7634 (mtm) cc_final: 0.6025 (mtm) REVERT: X 544 MET cc_start: 0.7646 (mmp) cc_final: 0.7185 (mmp) REVERT: X 549 MET cc_start: 0.8682 (mpp) cc_final: 0.8450 (mmp) REVERT: X 552 PHE cc_start: 0.8211 (t80) cc_final: 0.7297 (t80) REVERT: X 554 LYS cc_start: 0.9001 (tmtt) cc_final: 0.8722 (tptp) REVERT: X 662 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8302 (pt0) REVERT: X 738 LYS cc_start: 0.8523 (mmpt) cc_final: 0.8162 (mmmt) REVERT: X 748 ASP cc_start: 0.8986 (t0) cc_final: 0.8682 (t0) REVERT: X 772 MET cc_start: 0.8564 (mtm) cc_final: 0.7882 (mtm) REVERT: Y 1 MET cc_start: 0.7164 (tpt) cc_final: 0.6575 (tpt) REVERT: Y 94 GLU cc_start: 0.7847 (tt0) cc_final: 0.6673 (tm-30) REVERT: Y 101 ARG cc_start: 0.7893 (mpt180) cc_final: 0.6493 (mpt180) REVERT: Y 107 LEU cc_start: 0.8053 (tp) cc_final: 0.7788 (mm) REVERT: Y 116 ASN cc_start: 0.7810 (m-40) cc_final: 0.7249 (t0) REVERT: Y 128 LEU cc_start: 0.6864 (tt) cc_final: 0.6522 (pp) REVERT: Y 142 ASP cc_start: 0.6422 (t0) cc_final: 0.5995 (t0) REVERT: Y 151 SER cc_start: 0.6945 (p) cc_final: 0.6698 (p) REVERT: Y 170 HIS cc_start: 0.7755 (t70) cc_final: 0.7190 (t70) REVERT: Y 204 ASP cc_start: 0.7533 (m-30) cc_final: 0.7256 (m-30) REVERT: Y 208 ILE cc_start: 0.8581 (tt) cc_final: 0.8374 (mm) REVERT: Y 213 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7153 (mm-30) REVERT: Y 338 VAL cc_start: 0.8020 (p) cc_final: 0.7700 (m) REVERT: Y 346 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8333 (ptmm) REVERT: Y 363 ARG cc_start: 0.7915 (ttt180) cc_final: 0.7247 (ttp-170) REVERT: Y 444 LEU cc_start: 0.8632 (tp) cc_final: 0.8157 (pp) REVERT: Y 505 PHE cc_start: 0.8148 (m-10) cc_final: 0.7831 (m-80) REVERT: Y 527 MET cc_start: 0.8432 (mmt) cc_final: 0.8172 (mmm) REVERT: Y 552 PHE cc_start: 0.6912 (t80) cc_final: 0.6540 (t80) REVERT: Y 591 TRP cc_start: 0.7892 (m-90) cc_final: 0.7210 (m-90) REVERT: Y 617 ARG cc_start: 0.8736 (tpm170) cc_final: 0.8356 (tpm170) REVERT: Y 655 THR cc_start: 0.8629 (p) cc_final: 0.8362 (p) REVERT: Y 694 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7606 (mmmt) REVERT: Y 762 ILE cc_start: 0.8086 (pt) cc_final: 0.7825 (pt) REVERT: Z 11 THR cc_start: 0.8335 (m) cc_final: 0.7656 (m) REVERT: Z 14 TYR cc_start: 0.7551 (p90) cc_final: 0.6711 (p90) REVERT: Z 189 TYR cc_start: 0.8538 (m-80) cc_final: 0.7811 (m-10) REVERT: Z 199 MET cc_start: 0.8524 (mmp) cc_final: 0.8200 (tpp) REVERT: Z 215 LYS cc_start: 0.7961 (mppt) cc_final: 0.7191 (mmtt) REVERT: Z 219 TYR cc_start: 0.7912 (m-10) cc_final: 0.7508 (m-80) REVERT: Z 265 MET cc_start: 0.7100 (mpp) cc_final: 0.5621 (mpp) REVERT: Z 267 TYR cc_start: 0.7408 (m-80) cc_final: 0.7101 (m-80) REVERT: Z 338 VAL cc_start: 0.7158 (t) cc_final: 0.6899 (p) REVERT: Z 380 CYS cc_start: 0.7790 (t) cc_final: 0.7566 (p) REVERT: Z 421 LEU cc_start: 0.8021 (mt) cc_final: 0.7772 (mt) REVERT: Z 428 PHE cc_start: 0.8128 (m-10) cc_final: 0.7835 (m-80) REVERT: Z 441 ARG cc_start: 0.7371 (ptt180) cc_final: 0.6932 (ptt180) REVERT: Z 530 MET cc_start: 0.8779 (tpt) cc_final: 0.8369 (tpp) REVERT: Z 549 MET cc_start: 0.7992 (ppp) cc_final: 0.7527 (ppp) REVERT: Z 550 LYS cc_start: 0.8568 (tmtt) cc_final: 0.8221 (tptp) REVERT: Z 551 LYS cc_start: 0.8083 (ptpt) cc_final: 0.7731 (ptpt) REVERT: Z 617 ARG cc_start: 0.8189 (ptm160) cc_final: 0.7850 (ptm160) REVERT: Z 620 ARG cc_start: 0.8525 (mtp180) cc_final: 0.7928 (ptp-170) REVERT: Z 622 LYS cc_start: 0.8546 (mmpt) cc_final: 0.8160 (mmpt) REVERT: Z 623 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8029 (mm-30) REVERT: Z 624 MET cc_start: 0.8140 (ptp) cc_final: 0.7595 (ptp) REVERT: Z 627 GLN cc_start: 0.7777 (pp30) cc_final: 0.7211 (pp30) REVERT: Z 629 GLU cc_start: 0.7870 (mp0) cc_final: 0.7376 (mp0) REVERT: Z 666 LYS cc_start: 0.8790 (tptm) cc_final: 0.8489 (tptp) REVERT: Z 673 TYR cc_start: 0.7213 (m-10) cc_final: 0.6768 (m-10) REVERT: Z 721 ILE cc_start: 0.7999 (mp) cc_final: 0.7191 (mp) REVERT: Z 722 ILE cc_start: 0.7472 (mm) cc_final: 0.6916 (tp) REVERT: Z 768 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7698 (pt0) outliers start: 0 outliers final: 0 residues processed: 416 average time/residue: 0.3507 time to fit residues: 209.4298 Evaluate side-chains 375 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 188 optimal weight: 0.8980 chunk 201 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 157 optimal weight: 0.0870 chunk 61 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 190 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 773 GLN ** Y 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 436 HIS ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 18116 Z= 0.284 Angle : 0.814 10.892 24626 Z= 0.422 Chirality : 0.051 0.209 2820 Planarity : 0.006 0.083 3186 Dihedral : 6.391 32.264 2447 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 27.71 Ramachandran Plot: Outliers : 0.27 % Allowed : 12.97 % Favored : 86.76 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.50 (0.17), residues: 2244 helix: -0.81 (0.21), residues: 561 sheet: -2.47 (0.22), residues: 474 loop : -3.09 (0.16), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Y 262 HIS 0.022 0.003 HIS Y 170 PHE 0.026 0.002 PHE Z 140 TYR 0.030 0.002 TYR X 194 ARG 0.010 0.001 ARG Z 491 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 1.927 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 18 LEU cc_start: 0.8312 (mt) cc_final: 0.8045 (mt) REVERT: X 40 PHE cc_start: 0.7358 (p90) cc_final: 0.6762 (p90) REVERT: X 42 GLN cc_start: 0.8940 (pm20) cc_final: 0.8738 (pm20) REVERT: X 75 ASN cc_start: 0.8051 (p0) cc_final: 0.7401 (p0) REVERT: X 138 TRP cc_start: 0.7623 (m100) cc_final: 0.6975 (m100) REVERT: X 215 LYS cc_start: 0.8114 (mppt) cc_final: 0.7689 (mtmm) REVERT: X 219 TYR cc_start: 0.8160 (m-80) cc_final: 0.7884 (m-80) REVERT: X 222 ASN cc_start: 0.8563 (m-40) cc_final: 0.8100 (p0) REVERT: X 291 TRP cc_start: 0.7648 (m-10) cc_final: 0.7116 (m-10) REVERT: X 293 GLU cc_start: 0.6189 (pp20) cc_final: 0.5836 (pp20) REVERT: X 296 PHE cc_start: 0.7147 (m-80) cc_final: 0.6853 (m-10) REVERT: X 375 LEU cc_start: 0.8185 (mm) cc_final: 0.7985 (mm) REVERT: X 376 ASN cc_start: 0.7764 (t0) cc_final: 0.7367 (t0) REVERT: X 491 ARG cc_start: 0.7470 (mtt180) cc_final: 0.7085 (mtt-85) REVERT: X 527 MET cc_start: 0.7868 (mtm) cc_final: 0.6400 (mtm) REVERT: X 544 MET cc_start: 0.7582 (mmp) cc_final: 0.7085 (mmp) REVERT: X 549 MET cc_start: 0.8966 (mpp) cc_final: 0.8657 (mmt) REVERT: X 552 PHE cc_start: 0.8443 (t80) cc_final: 0.7583 (t80) REVERT: X 554 LYS cc_start: 0.9130 (tmtt) cc_final: 0.8854 (tptp) REVERT: X 620 ARG cc_start: 0.8380 (mtm-85) cc_final: 0.8127 (ptt-90) REVERT: X 623 GLU cc_start: 0.8185 (mp0) cc_final: 0.7771 (mm-30) REVERT: X 662 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8274 (pt0) REVERT: X 666 LYS cc_start: 0.8601 (pptt) cc_final: 0.8311 (ptmm) REVERT: X 710 ASP cc_start: 0.8648 (m-30) cc_final: 0.8347 (m-30) REVERT: X 722 ILE cc_start: 0.7944 (mm) cc_final: 0.7579 (tp) REVERT: X 727 LEU cc_start: 0.8562 (mm) cc_final: 0.8258 (mm) REVERT: X 738 LYS cc_start: 0.8586 (mmpt) cc_final: 0.8283 (mmmt) REVERT: X 748 ASP cc_start: 0.9061 (t0) cc_final: 0.8664 (t0) REVERT: X 772 MET cc_start: 0.8601 (mtm) cc_final: 0.7961 (mtm) REVERT: Y 1 MET cc_start: 0.7274 (tpt) cc_final: 0.6739 (tpt) REVERT: Y 94 GLU cc_start: 0.7986 (tt0) cc_final: 0.6855 (tm-30) REVERT: Y 101 ARG cc_start: 0.8137 (mpt180) cc_final: 0.6869 (mpt180) REVERT: Y 107 LEU cc_start: 0.8168 (tp) cc_final: 0.7913 (mm) REVERT: Y 116 ASN cc_start: 0.7942 (m-40) cc_final: 0.7344 (t0) REVERT: Y 128 LEU cc_start: 0.7299 (tt) cc_final: 0.6772 (pp) REVERT: Y 142 ASP cc_start: 0.6772 (t0) cc_final: 0.6293 (t0) REVERT: Y 151 SER cc_start: 0.7180 (p) cc_final: 0.6916 (p) REVERT: Y 159 LEU cc_start: 0.9284 (mp) cc_final: 0.9060 (tp) REVERT: Y 170 HIS cc_start: 0.7714 (t70) cc_final: 0.7402 (t70) REVERT: Y 213 GLU cc_start: 0.7609 (mt-10) cc_final: 0.6853 (mm-30) REVERT: Y 216 CYS cc_start: 0.8824 (t) cc_final: 0.8596 (t) REVERT: Y 338 VAL cc_start: 0.8057 (p) cc_final: 0.7720 (m) REVERT: Y 346 LYS cc_start: 0.8672 (ptpp) cc_final: 0.8413 (ptmm) REVERT: Y 444 LEU cc_start: 0.8742 (tp) cc_final: 0.8298 (pp) REVERT: Y 454 ASP cc_start: 0.3677 (p0) cc_final: 0.2904 (p0) REVERT: Y 491 ARG cc_start: 0.8426 (mmp-170) cc_final: 0.8220 (mmm160) REVERT: Y 503 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7625 (mt-10) REVERT: Y 505 PHE cc_start: 0.8259 (m-10) cc_final: 0.7941 (m-80) REVERT: Y 552 PHE cc_start: 0.7098 (t80) cc_final: 0.6614 (t80) REVERT: Y 617 ARG cc_start: 0.8811 (tpm170) cc_final: 0.8555 (tpm170) REVERT: Y 694 LYS cc_start: 0.8118 (mmmt) cc_final: 0.7591 (mmmt) REVERT: Y 707 LYS cc_start: 0.9166 (tttm) cc_final: 0.8896 (tttp) REVERT: Y 729 ASN cc_start: 0.8362 (t0) cc_final: 0.8143 (t0) REVERT: Y 762 ILE cc_start: 0.8034 (pt) cc_final: 0.7475 (pt) REVERT: Z 11 THR cc_start: 0.8465 (m) cc_final: 0.7904 (m) REVERT: Z 14 TYR cc_start: 0.7809 (p90) cc_final: 0.7021 (p90) REVERT: Z 189 TYR cc_start: 0.8679 (m-80) cc_final: 0.7963 (m-80) REVERT: Z 215 LYS cc_start: 0.8089 (mppt) cc_final: 0.7324 (mttt) REVERT: Z 219 TYR cc_start: 0.7912 (m-10) cc_final: 0.7391 (m-80) REVERT: Z 265 MET cc_start: 0.7077 (mpp) cc_final: 0.5601 (mpp) REVERT: Z 267 TYR cc_start: 0.7670 (m-80) cc_final: 0.7290 (m-80) REVERT: Z 341 LYS cc_start: 0.7769 (tppt) cc_final: 0.7496 (tppt) REVERT: Z 352 TYR cc_start: 0.7385 (m-10) cc_final: 0.7027 (m-10) REVERT: Z 380 CYS cc_start: 0.8362 (t) cc_final: 0.8141 (p) REVERT: Z 421 LEU cc_start: 0.8544 (mt) cc_final: 0.8331 (mt) REVERT: Z 422 ASN cc_start: 0.7739 (p0) cc_final: 0.7378 (p0) REVERT: Z 428 PHE cc_start: 0.8109 (m-10) cc_final: 0.7197 (m-10) REVERT: Z 477 ASN cc_start: 0.8339 (t0) cc_final: 0.7956 (t0) REVERT: Z 479 ASP cc_start: 0.8566 (m-30) cc_final: 0.7736 (m-30) REVERT: Z 530 MET cc_start: 0.8800 (tpt) cc_final: 0.8381 (tpp) REVERT: Z 549 MET cc_start: 0.8227 (ppp) cc_final: 0.7088 (ppp) REVERT: Z 550 LYS cc_start: 0.8679 (tmtt) cc_final: 0.8461 (mmtp) REVERT: Z 551 LYS cc_start: 0.8265 (ptpt) cc_final: 0.7869 (ptpt) REVERT: Z 617 ARG cc_start: 0.8198 (ptm160) cc_final: 0.7814 (ptm160) REVERT: Z 622 LYS cc_start: 0.8645 (mmpt) cc_final: 0.8265 (mmpt) REVERT: Z 623 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8112 (mm-30) REVERT: Z 624 MET cc_start: 0.8224 (ptp) cc_final: 0.7730 (ptp) REVERT: Z 627 GLN cc_start: 0.7806 (pp30) cc_final: 0.7130 (pp30) REVERT: Z 629 GLU cc_start: 0.7938 (mp0) cc_final: 0.7398 (mp0) REVERT: Z 647 LYS cc_start: 0.8462 (tptm) cc_final: 0.8022 (pttt) REVERT: Z 666 LYS cc_start: 0.8879 (tptm) cc_final: 0.8584 (tptp) REVERT: Z 673 TYR cc_start: 0.7530 (m-10) cc_final: 0.6985 (m-10) REVERT: Z 721 ILE cc_start: 0.8010 (mp) cc_final: 0.7557 (mp) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.3517 time to fit residues: 205.9760 Evaluate side-chains 361 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 1.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 6.9990 chunk 212 optimal weight: 0.0020 chunk 129 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 147 optimal weight: 0.5980 chunk 223 optimal weight: 0.9990 chunk 205 optimal weight: 0.0980 chunk 177 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 137 optimal weight: 0.4980 chunk 108 optimal weight: 6.9990 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 188 HIS ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN ** Y 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 436 HIS ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18116 Z= 0.213 Angle : 0.811 10.632 24626 Z= 0.410 Chirality : 0.051 0.309 2820 Planarity : 0.006 0.080 3186 Dihedral : 6.119 33.207 2447 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 20.91 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.83 % Favored : 88.90 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.17), residues: 2244 helix: -0.73 (0.21), residues: 561 sheet: -2.30 (0.22), residues: 482 loop : -2.98 (0.17), residues: 1201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP Y 262 HIS 0.010 0.002 HIS Y 315 PHE 0.028 0.002 PHE Z 140 TYR 0.026 0.002 TYR Y 462 ARG 0.015 0.001 ARG X 775 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4488 Ramachandran restraints generated. 2244 Oldfield, 0 Emsley, 2244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 1.914 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 10 LEU cc_start: 0.8362 (tt) cc_final: 0.8127 (tt) REVERT: X 18 LEU cc_start: 0.8380 (mt) cc_final: 0.8125 (mt) REVERT: X 40 PHE cc_start: 0.7121 (p90) cc_final: 0.6553 (p90) REVERT: X 74 PHE cc_start: 0.8704 (t80) cc_final: 0.8416 (t80) REVERT: X 75 ASN cc_start: 0.7896 (p0) cc_final: 0.7148 (p0) REVERT: X 138 TRP cc_start: 0.7121 (m100) cc_final: 0.6613 (m100) REVERT: X 215 LYS cc_start: 0.8002 (mppt) cc_final: 0.7597 (mtmm) REVERT: X 219 TYR cc_start: 0.7930 (m-80) cc_final: 0.7580 (m-80) REVERT: X 222 ASN cc_start: 0.8301 (m-40) cc_final: 0.7856 (p0) REVERT: X 291 TRP cc_start: 0.7380 (m-10) cc_final: 0.6911 (m-10) REVERT: X 317 THR cc_start: 0.5661 (m) cc_final: 0.5274 (m) REVERT: X 375 LEU cc_start: 0.8023 (mm) cc_final: 0.7808 (mm) REVERT: X 414 GLN cc_start: 0.8339 (tp-100) cc_final: 0.7275 (tp40) REVERT: X 491 ARG cc_start: 0.7521 (mtt180) cc_final: 0.7239 (mtt-85) REVERT: X 527 MET cc_start: 0.7677 (mtm) cc_final: 0.6031 (mtm) REVERT: X 544 MET cc_start: 0.7488 (mmp) cc_final: 0.7023 (mmp) REVERT: X 552 PHE cc_start: 0.8043 (t80) cc_final: 0.7224 (t80) REVERT: X 554 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8702 (tptp) REVERT: X 611 GLN cc_start: 0.8874 (mt0) cc_final: 0.8669 (mt0) REVERT: X 620 ARG cc_start: 0.8100 (mtm-85) cc_final: 0.7801 (ptt-90) REVERT: X 662 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8285 (pt0) REVERT: X 666 LYS cc_start: 0.8413 (pptt) cc_final: 0.8132 (ptmm) REVERT: X 710 ASP cc_start: 0.8574 (m-30) cc_final: 0.8255 (m-30) REVERT: X 738 LYS cc_start: 0.8532 (mmpt) cc_final: 0.8173 (mmmt) REVERT: X 748 ASP cc_start: 0.8940 (t0) cc_final: 0.8552 (t0) REVERT: X 759 ASP cc_start: 0.8515 (t70) cc_final: 0.8252 (t0) REVERT: X 770 LEU cc_start: 0.9306 (mt) cc_final: 0.9043 (mt) REVERT: X 772 MET cc_start: 0.8509 (mtm) cc_final: 0.7791 (mtm) REVERT: Y 1 MET cc_start: 0.7137 (tpt) cc_final: 0.6791 (tpt) REVERT: Y 5 ILE cc_start: 0.7973 (mm) cc_final: 0.7724 (mm) REVERT: Y 94 GLU cc_start: 0.7839 (tt0) cc_final: 0.6767 (tm-30) REVERT: Y 101 ARG cc_start: 0.7928 (mpt180) cc_final: 0.6429 (mmt-90) REVERT: Y 116 ASN cc_start: 0.7779 (m-40) cc_final: 0.7292 (t0) REVERT: Y 128 LEU cc_start: 0.7004 (tt) cc_final: 0.6570 (pp) REVERT: Y 142 ASP cc_start: 0.6488 (t0) cc_final: 0.6033 (t0) REVERT: Y 151 SER cc_start: 0.6987 (p) cc_final: 0.6727 (p) REVERT: Y 170 HIS cc_start: 0.7666 (t70) cc_final: 0.7293 (t70) REVERT: Y 208 ILE cc_start: 0.8624 (mm) cc_final: 0.8387 (tp) REVERT: Y 213 GLU cc_start: 0.7382 (mt-10) cc_final: 0.7168 (mm-30) REVERT: Y 338 VAL cc_start: 0.7872 (p) cc_final: 0.7601 (m) REVERT: Y 363 ARG cc_start: 0.7886 (ttt180) cc_final: 0.7656 (ttt180) REVERT: Y 433 GLU cc_start: 0.7120 (pt0) cc_final: 0.6710 (pt0) REVERT: Y 444 LEU cc_start: 0.8653 (tp) cc_final: 0.8170 (pp) REVERT: Y 500 GLU cc_start: 0.7354 (mp0) cc_final: 0.6806 (pm20) REVERT: Y 503 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7572 (mt-10) REVERT: Y 527 MET cc_start: 0.8360 (mmp) cc_final: 0.8107 (mmm) REVERT: Y 547 ASN cc_start: 0.8439 (m-40) cc_final: 0.8236 (m-40) REVERT: Y 552 PHE cc_start: 0.6900 (t80) cc_final: 0.6509 (t80) REVERT: Y 568 LEU cc_start: 0.9348 (mt) cc_final: 0.8940 (mt) REVERT: Y 617 ARG cc_start: 0.8636 (tpm170) cc_final: 0.8371 (tpm170) REVERT: Y 694 LYS cc_start: 0.8103 (mmmt) cc_final: 0.7629 (mmmt) REVERT: Y 707 LYS cc_start: 0.9082 (tttm) cc_final: 0.8702 (tttp) REVERT: Z 14 TYR cc_start: 0.7578 (p90) cc_final: 0.6684 (p90) REVERT: Z 189 TYR cc_start: 0.8558 (m-80) cc_final: 0.7828 (m-10) REVERT: Z 215 LYS cc_start: 0.8009 (mppt) cc_final: 0.7382 (mmmt) REVERT: Z 219 TYR cc_start: 0.7792 (m-10) cc_final: 0.7329 (m-80) REVERT: Z 341 LYS cc_start: 0.7786 (tppt) cc_final: 0.7445 (tppt) REVERT: Z 379 MET cc_start: 0.7682 (pmm) cc_final: 0.7172 (pmm) REVERT: Z 380 CYS cc_start: 0.8278 (t) cc_final: 0.7851 (p) REVERT: Z 422 ASN cc_start: 0.7389 (p0) cc_final: 0.7079 (p0) REVERT: Z 479 ASP cc_start: 0.8443 (m-30) cc_final: 0.7892 (m-30) REVERT: Z 530 MET cc_start: 0.8746 (tpt) cc_final: 0.8326 (tpp) REVERT: Z 550 LYS cc_start: 0.8552 (tmtt) cc_final: 0.8293 (tptp) REVERT: Z 551 LYS cc_start: 0.8179 (ptpt) cc_final: 0.7849 (ptpt) REVERT: Z 617 ARG cc_start: 0.8190 (ptm160) cc_final: 0.7859 (ptm160) REVERT: Z 620 ARG cc_start: 0.8578 (mtp180) cc_final: 0.7989 (ptp-170) REVERT: Z 622 LYS cc_start: 0.8584 (mmpt) cc_final: 0.8229 (mmpt) REVERT: Z 623 GLU cc_start: 0.8978 (mm-30) cc_final: 0.7899 (mm-30) REVERT: Z 624 MET cc_start: 0.8193 (ptp) cc_final: 0.7672 (ptp) REVERT: Z 629 GLU cc_start: 0.8004 (mp0) cc_final: 0.7718 (mp0) REVERT: Z 673 TYR cc_start: 0.7248 (m-10) cc_final: 0.6959 (m-10) REVERT: Z 721 ILE cc_start: 0.8019 (mp) cc_final: 0.7311 (mp) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.3414 time to fit residues: 198.2443 Evaluate side-chains 346 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 2.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 6.9990 chunk 189 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.4980 chunk 177 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 182 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 188 HIS X 193 ASN ** X 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 266 GLN ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN ** Y 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 302 GLN Y 324 ASN Y 436 HIS ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 113 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.148689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.114725 restraints weight = 56433.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.119402 restraints weight = 41454.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.123066 restraints weight = 32176.011| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3823 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3823 r_free = 0.3823 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6853 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18116 Z= 0.204 Angle : 0.798 11.336 24626 Z= 0.404 Chirality : 0.051 0.292 2820 Planarity : 0.006 0.080 3186 Dihedral : 5.983 31.588 2447 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.63 % Favored : 88.10 % Rotamer: Outliers : 0.05 % Allowed : 0.60 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.17), residues: 2244 helix: -0.73 (0.21), residues: 558 sheet: -2.19 (0.22), residues: 499 loop : -3.00 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP X 356 HIS 0.019 0.002 HIS Y 170 PHE 0.042 0.002 PHE Y 505 TYR 0.023 0.001 TYR Y 462 ARG 0.017 0.001 ARG Z 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4407.24 seconds wall clock time: 81 minutes 24.79 seconds (4884.79 seconds total)