Starting phenix.real_space_refine on Sun Aug 24 06:54:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ole_16956/08_2025/8ole_16956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ole_16956/08_2025/8ole_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ole_16956/08_2025/8ole_16956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ole_16956/08_2025/8ole_16956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ole_16956/08_2025/8ole_16956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ole_16956/08_2025/8ole_16956.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.87, per 1000 atoms: 0.22 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 741.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.50 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: 3.35 Time building geometry restraints manager: 2.10 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: 42 2.22 - 2.89: 7676 2.89 - 3.56: 28014 3.56 - 4.23: 43419 4.23 - 4.90: 68983 Nonbonded interactions: 148134 Sorted by model distance: nonbonded pdb=" NH2 ARG Z 620 " pdb=" O ALA Z 684 " model vdw 1.554 3.120 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 nonbonded pdb=" CB ASN X 171 " pdb=" NH1 ARG X 210 " model vdw 2.066 3.520 ... (remaining 148129 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: 0.780 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.400 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.210 ------------------------------------------------------------------------------- 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 : 0.005 0.378 18117 Z= 0.357 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 : 30.01 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.001 ARG X 429 TYR 0.042 0.002 TYR X 219 PHE 0.023 0.002 PHE X 505 TRP 0.027 0.002 TRP X 356 HIS 0.009 0.002 HIS Y 315 Details of bonding type rmsd covalent geometry : bond 0.00397 (18116) covalent geometry : angle 0.90202 (24626) hydrogen bonds : bond 0.24680 ( 550) hydrogen bonds : angle 9.19458 ( 1524) Misc. bond : bond 0.37834 ( 1) *********************** 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 : 0.476 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: 0.1369 time to fit residues: 88.2409 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 : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.2980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.2980 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 180 GLN X 183 ASN ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 249 GLN ** X 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 302 GLN ** X 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN ** Y 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 457 ASN Y 506 ASN Z 8 GLN Z 97 ASN ** Z 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 364 ASN Z 456 ASN ** Z 492 GLN ** 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.152220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.119067 restraints weight = 58864.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.124088 restraints weight = 42493.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.127970 restraints weight = 32338.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.130965 restraints weight = 25561.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.133266 restraints weight = 20831.781| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 18117 Z= 0.154 Angle : 0.776 9.973 24626 Z= 0.402 Chirality : 0.050 0.191 2820 Planarity : 0.006 0.070 3186 Dihedral : 6.425 27.166 2447 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.14 % Favored : 88.59 % Rotamer: Outliers : 0.15 % Allowed : 6.53 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.66 (0.16), residues: 2244 helix: -1.14 (0.20), residues: 567 sheet: -2.29 (0.22), residues: 498 loop : -3.24 (0.16), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 185 TYR 0.028 0.002 TYR X 219 PHE 0.029 0.002 PHE Y 505 TRP 0.029 0.002 TRP Y 262 HIS 0.010 0.002 HIS Y 170 Details of bonding type rmsd covalent geometry : bond 0.00340 (18116) covalent geometry : angle 0.77622 (24626) hydrogen bonds : bond 0.05257 ( 550) hydrogen bonds : angle 6.88617 ( 1524) Misc. bond : bond 0.00030 ( 1) *********************** 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: 3 poor density : 430 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 40 PHE cc_start: 0.7737 (p90) cc_final: 0.6833 (p90) REVERT: X 42 GLN cc_start: 0.9096 (pm20) cc_final: 0.8785 (pm20) REVERT: X 70 GLN cc_start: 0.7408 (mp10) cc_final: 0.6985 (mp10) REVERT: X 75 ASN cc_start: 0.8455 (p0) cc_final: 0.7875 (p0) REVERT: X 77 PRO cc_start: 0.6504 (Cg_exo) cc_final: 0.6111 (Cg_endo) REVERT: X 100 ASP cc_start: 0.6443 (t0) cc_final: 0.6118 (t0) REVERT: X 219 TYR cc_start: 0.8455 (m-80) cc_final: 0.8067 (m-80) REVERT: X 251 ASN cc_start: 0.7778 (m110) cc_final: 0.7387 (m110) REVERT: X 265 MET cc_start: 0.4607 (mpp) cc_final: 0.4154 (mpp) REVERT: X 356 TRP cc_start: 0.6804 (m100) cc_final: 0.6291 (m100) REVERT: X 375 LEU cc_start: 0.8244 (mm) cc_final: 0.7933 (mm) REVERT: X 393 GLN cc_start: 0.8800 (mp10) cc_final: 0.8124 (tp-100) REVERT: X 394 TRP cc_start: 0.8108 (m-10) cc_final: 0.7817 (m-10) REVERT: X 477 ASN cc_start: 0.8644 (p0) cc_final: 0.8360 (p0) REVERT: X 527 MET cc_start: 0.8210 (mtm) cc_final: 0.6935 (mtm) REVERT: X 549 MET cc_start: 0.9133 (mpp) cc_final: 0.8793 (mmm) REVERT: X 552 PHE cc_start: 0.8924 (t80) cc_final: 0.7795 (t80) REVERT: X 615 ILE cc_start: 0.8566 (pt) cc_final: 0.8294 (mt) REVERT: X 617 ARG cc_start: 0.8582 (mmt-90) cc_final: 0.8215 (mpt180) REVERT: X 620 ARG cc_start: 0.9145 (ptm-80) cc_final: 0.8878 (ptm-80) REVERT: X 623 GLU cc_start: 0.8244 (mp0) cc_final: 0.7788 (mm-30) REVERT: X 666 LYS cc_start: 0.8583 (ptmm) cc_final: 0.8221 (tptp) REVERT: X 673 TYR cc_start: 0.8397 (m-80) cc_final: 0.8177 (m-80) REVERT: X 738 LYS cc_start: 0.8309 (mmpt) cc_final: 0.8109 (mmmt) REVERT: X 748 ASP cc_start: 0.8980 (t0) cc_final: 0.8669 (t0) REVERT: X 755 PHE cc_start: 0.8406 (m-80) cc_final: 0.7717 (m-10) REVERT: X 772 MET cc_start: 0.8636 (mtm) cc_final: 0.8117 (mtm) REVERT: X 773 GLN cc_start: 0.9012 (pt0) cc_final: 0.8808 (pt0) REVERT: Y 40 PHE cc_start: 0.7716 (t80) cc_final: 0.7498 (t80) REVERT: Y 69 TYR cc_start: 0.7861 (m-80) cc_final: 0.7619 (m-80) REVERT: Y 84 LEU cc_start: 0.8556 (mt) cc_final: 0.8344 (mt) REVERT: Y 94 GLU cc_start: 0.8022 (tt0) cc_final: 0.6787 (tm-30) REVERT: Y 116 ASN cc_start: 0.8027 (m-40) cc_final: 0.7555 (t0) REVERT: Y 128 LEU cc_start: 0.7796 (tt) cc_final: 0.7145 (pp) REVERT: Y 142 ASP cc_start: 0.7300 (t0) cc_final: 0.6557 (t0) REVERT: Y 159 LEU cc_start: 0.9349 (mp) cc_final: 0.8919 (tp) REVERT: Y 246 TYR cc_start: 0.7332 (t80) cc_final: 0.6846 (t80) REVERT: Y 265 MET cc_start: 0.7803 (mmp) cc_final: 0.7083 (tpt) REVERT: Y 267 TYR cc_start: 0.6930 (m-10) cc_final: 0.6223 (m-10) REVERT: Y 274 ARG cc_start: 0.7491 (ttt180) cc_final: 0.7270 (ttm170) REVERT: Y 277 PHE cc_start: 0.7543 (t80) cc_final: 0.6652 (t80) REVERT: Y 297 LYS cc_start: 0.8350 (mmpt) cc_final: 0.7953 (mmtm) REVERT: Y 356 TRP cc_start: 0.6659 (m-10) cc_final: 0.6112 (m-90) REVERT: Y 405 HIS cc_start: 0.8355 (p90) cc_final: 0.7952 (p90) REVERT: Y 434 GLU cc_start: 0.8327 (mp0) cc_final: 0.7906 (mm-30) REVERT: Y 444 LEU cc_start: 0.9032 (tp) cc_final: 0.8440 (pp) REVERT: Y 462 TYR cc_start: 0.6547 (m-80) cc_final: 0.4306 (m-80) REVERT: Y 512 ILE cc_start: 0.8610 (pt) cc_final: 0.8384 (pt) REVERT: Y 530 MET cc_start: 0.8152 (tpt) cc_final: 0.7436 (tpt) REVERT: Y 591 TRP cc_start: 0.8257 (m-90) cc_final: 0.7584 (m-90) REVERT: Y 611 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: Y 617 ARG cc_start: 0.8646 (tpm170) cc_final: 0.8446 (tpm170) REVERT: Y 618 ARG cc_start: 0.9243 (mtp180) cc_final: 0.8919 (ttp-170) REVERT: Y 762 ILE cc_start: 0.8288 (pt) cc_final: 0.7878 (pt) REVERT: Z 14 TYR cc_start: 0.7946 (p90) cc_final: 0.7011 (p90) REVERT: Z 189 TYR cc_start: 0.9472 (m-10) cc_final: 0.9200 (m-10) REVERT: Z 199 MET cc_start: 0.8719 (mmp) cc_final: 0.7891 (tmm) REVERT: Z 215 LYS cc_start: 0.7385 (mppt) cc_final: 0.7039 (mmtt) REVERT: Z 219 TYR cc_start: 0.7386 (m-10) cc_final: 0.6926 (m-80) REVERT: Z 267 TYR cc_start: 0.8074 (m-80) cc_final: 0.7269 (m-80) REVERT: Z 464 ILE cc_start: 0.9153 (mp) cc_final: 0.8688 (mp) REVERT: Z 500 GLU cc_start: 0.8598 (pp20) cc_final: 0.8275 (pp20) REVERT: Z 514 MET cc_start: 0.7018 (tmm) cc_final: 0.6680 (tmm) REVERT: Z 527 MET cc_start: 0.8272 (ptm) cc_final: 0.7782 (pmm) REVERT: Z 530 MET cc_start: 0.9030 (tpt) cc_final: 0.8722 (tpp) REVERT: Z 617 ARG cc_start: 0.8052 (ptm160) cc_final: 0.7844 (ptm160) REVERT: Z 620 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7613 (mtp85) REVERT: Z 623 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8283 (mm-30) REVERT: Z 624 MET cc_start: 0.7676 (ptp) cc_final: 0.7228 (ptp) REVERT: Z 673 TYR cc_start: 0.7782 (m-10) cc_final: 0.7399 (m-10) REVERT: Z 721 ILE cc_start: 0.7745 (mp) cc_final: 0.7082 (mp) outliers start: 3 outliers final: 0 residues processed: 433 average time/residue: 0.1481 time to fit residues: 93.0350 Evaluate side-chains 364 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 74 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 72 optimal weight: 7.9990 chunk 195 optimal weight: 9.9990 chunk 45 optimal weight: 0.0470 chunk 80 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 overall best weight: 1.0084 ------------------------------------------------------------------------------- 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 X 315 HIS ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 497 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN Y 180 GLN ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 506 ASN ** Y 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 456 ASN Z 757 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.149033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.116740 restraints weight = 52742.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.121561 restraints weight = 37442.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.125342 restraints weight = 28285.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.128342 restraints weight = 22252.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.130671 restraints weight = 18030.311| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6664 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 18117 Z= 0.144 Angle : 0.749 10.597 24626 Z= 0.385 Chirality : 0.049 0.193 2820 Planarity : 0.006 0.079 3186 Dihedral : 6.256 28.289 2447 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.54 % Favored : 88.19 % Rotamer: Outliers : 0.00 % Allowed : 5.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (0.16), residues: 2244 helix: -1.06 (0.20), residues: 569 sheet: -2.16 (0.22), residues: 499 loop : -3.22 (0.16), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 674 TYR 0.023 0.002 TYR X 219 PHE 0.028 0.002 PHE X 505 TRP 0.027 0.001 TRP Y 262 HIS 0.014 0.002 HIS Y 170 Details of bonding type rmsd covalent geometry : bond 0.00317 (18116) covalent geometry : angle 0.74915 (24626) hydrogen bonds : bond 0.04496 ( 550) hydrogen bonds : angle 6.44469 ( 1524) Misc. bond : bond 0.00062 ( 1) *********************** 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 403 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 403 time to evaluate : 0.446 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: X 1 MET cc_start: 0.7646 (mmm) cc_final: 0.7443 (mmm) REVERT: X 40 PHE cc_start: 0.7902 (p90) cc_final: 0.7289 (p90) REVERT: X 70 GLN cc_start: 0.7053 (mp10) cc_final: 0.6852 (mp10) REVERT: X 75 ASN cc_start: 0.8278 (p0) cc_final: 0.7685 (p0) REVERT: X 199 MET cc_start: 0.7886 (ppp) cc_final: 0.7443 (ppp) REVERT: X 219 TYR cc_start: 0.8473 (m-80) cc_final: 0.8218 (m-80) REVERT: X 222 ASN cc_start: 0.8900 (m-40) cc_final: 0.8440 (p0) REVERT: X 251 ASN cc_start: 0.7737 (m110) cc_final: 0.7469 (m-40) REVERT: X 265 MET cc_start: 0.4581 (mpp) cc_final: 0.4106 (mpp) REVERT: X 303 TYR cc_start: 0.6839 (m-10) cc_final: 0.6223 (m-80) REVERT: X 305 TYR cc_start: 0.7749 (m-10) cc_final: 0.7410 (m-10) REVERT: X 356 TRP cc_start: 0.6904 (m100) cc_final: 0.6493 (m100) REVERT: X 375 LEU cc_start: 0.8221 (mm) cc_final: 0.7967 (mm) REVERT: X 393 GLN cc_start: 0.8771 (mp10) cc_final: 0.8059 (tp-100) REVERT: X 394 TRP cc_start: 0.8066 (m-10) cc_final: 0.7665 (m-10) REVERT: X 404 LEU cc_start: 0.8342 (mp) cc_final: 0.7854 (pp) REVERT: X 413 THR cc_start: 0.8888 (m) cc_final: 0.8685 (t) REVERT: X 429 ARG cc_start: 0.8897 (ppt170) cc_final: 0.8472 (ttp80) REVERT: X 477 ASN cc_start: 0.8666 (p0) cc_final: 0.8354 (p0) REVERT: X 491 ARG cc_start: 0.7124 (mtt180) cc_final: 0.6701 (mtt-85) REVERT: X 494 LEU cc_start: 0.9274 (tp) cc_final: 0.9070 (tp) REVERT: X 527 MET cc_start: 0.8443 (mtm) cc_final: 0.7365 (mtm) REVERT: X 539 ASP cc_start: 0.9394 (t70) cc_final: 0.9192 (t0) REVERT: X 549 MET cc_start: 0.9109 (mpp) cc_final: 0.8771 (mmm) REVERT: X 550 LYS cc_start: 0.8519 (pttm) cc_final: 0.8113 (pttp) REVERT: X 552 PHE cc_start: 0.8924 (t80) cc_final: 0.7841 (t80) REVERT: X 554 LYS cc_start: 0.9334 (tmtt) cc_final: 0.9031 (tptp) REVERT: X 617 ARG cc_start: 0.8719 (mmt-90) cc_final: 0.8206 (mpt180) REVERT: X 620 ARG cc_start: 0.9168 (ptm-80) cc_final: 0.8846 (ptm-80) REVERT: X 621 LEU cc_start: 0.9390 (pp) cc_final: 0.8989 (pp) REVERT: X 623 GLU cc_start: 0.8393 (mp0) cc_final: 0.7931 (mm-30) REVERT: X 662 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8373 (pt0) REVERT: X 673 TYR cc_start: 0.8585 (m-80) cc_final: 0.8137 (m-80) REVERT: X 738 LYS cc_start: 0.8369 (mmpt) cc_final: 0.8116 (mmmt) REVERT: X 748 ASP cc_start: 0.9086 (t0) cc_final: 0.8759 (t0) REVERT: X 755 PHE cc_start: 0.8450 (m-80) cc_final: 0.7785 (m-10) REVERT: X 764 ARG cc_start: 0.9415 (mtm180) cc_final: 0.9194 (mtm180) REVERT: X 772 MET cc_start: 0.8651 (mtm) cc_final: 0.8014 (mtm) REVERT: X 775 ARG cc_start: 0.8455 (tmt170) cc_final: 0.7773 (ttp80) REVERT: Y 64 LEU cc_start: 0.9211 (pp) cc_final: 0.8985 (pp) REVERT: Y 69 TYR cc_start: 0.7892 (m-80) cc_final: 0.7668 (m-80) REVERT: Y 94 GLU cc_start: 0.8223 (tt0) cc_final: 0.7000 (tm-30) REVERT: Y 116 ASN cc_start: 0.8017 (m-40) cc_final: 0.7553 (t0) REVERT: Y 128 LEU cc_start: 0.7894 (tt) cc_final: 0.7244 (pp) REVERT: Y 142 ASP cc_start: 0.7363 (t0) cc_final: 0.6747 (t0) REVERT: Y 155 TYR cc_start: 0.7845 (m-10) cc_final: 0.7428 (m-10) REVERT: Y 159 LEU cc_start: 0.9326 (mp) cc_final: 0.8887 (tp) REVERT: Y 170 HIS cc_start: 0.8302 (t70) cc_final: 0.7706 (t70) REVERT: Y 208 ILE cc_start: 0.8956 (mm) cc_final: 0.8647 (tp) REVERT: Y 216 CYS cc_start: 0.9330 (t) cc_final: 0.9125 (t) REVERT: Y 263 LYS cc_start: 0.7528 (mmmt) cc_final: 0.7249 (tppt) REVERT: Y 265 MET cc_start: 0.7757 (mmp) cc_final: 0.6775 (mmm) REVERT: Y 275 PHE cc_start: 0.7159 (t80) cc_final: 0.6744 (t80) REVERT: Y 277 PHE cc_start: 0.7424 (t80) cc_final: 0.6886 (t80) REVERT: Y 297 LYS cc_start: 0.8325 (mmpt) cc_final: 0.7923 (mmtm) REVERT: Y 356 TRP cc_start: 0.6840 (m-10) cc_final: 0.6401 (m-90) REVERT: Y 405 HIS cc_start: 0.8300 (p90) cc_final: 0.8068 (p90) REVERT: Y 424 LEU cc_start: 0.8477 (tp) cc_final: 0.8276 (tp) REVERT: Y 444 LEU cc_start: 0.9093 (tp) cc_final: 0.8532 (pp) REVERT: Y 462 TYR cc_start: 0.5595 (m-80) cc_final: 0.5168 (m-80) REVERT: Y 505 PHE cc_start: 0.8900 (m-10) cc_final: 0.8601 (m-10) REVERT: Y 512 ILE cc_start: 0.8573 (pt) cc_final: 0.8356 (pt) REVERT: Y 539 ASP cc_start: 0.6692 (t0) cc_final: 0.6440 (t0) REVERT: Y 591 TRP cc_start: 0.8422 (m-90) cc_final: 0.7412 (m-90) REVERT: Y 611 GLN cc_start: 0.8851 (pm20) cc_final: 0.8227 (pm20) REVERT: Y 682 PHE cc_start: 0.8420 (m-80) cc_final: 0.8148 (m-80) REVERT: Y 729 ASN cc_start: 0.8475 (t0) cc_final: 0.8179 (t0) REVERT: Y 762 ILE cc_start: 0.8494 (pt) cc_final: 0.8040 (pt) REVERT: Z 9 LEU cc_start: 0.8427 (mt) cc_final: 0.8155 (mt) REVERT: Z 14 TYR cc_start: 0.7981 (p90) cc_final: 0.7033 (p90) REVERT: Z 189 TYR cc_start: 0.9382 (m-10) cc_final: 0.9072 (m-10) REVERT: Z 199 MET cc_start: 0.8728 (mmp) cc_final: 0.7960 (tmm) REVERT: Z 212 GLU cc_start: 0.8833 (mp0) cc_final: 0.8577 (mp0) REVERT: Z 215 LYS cc_start: 0.7458 (mppt) cc_final: 0.7058 (mmmt) REVERT: Z 219 TYR cc_start: 0.7747 (m-10) cc_final: 0.7245 (m-80) REVERT: Z 267 TYR cc_start: 0.8138 (m-80) cc_final: 0.7364 (m-80) REVERT: Z 342 PHE cc_start: 0.6843 (t80) cc_final: 0.6578 (t80) REVERT: Z 530 MET cc_start: 0.8940 (tpt) cc_final: 0.8663 (tpp) REVERT: Z 549 MET cc_start: 0.8657 (ppp) cc_final: 0.8306 (ppp) REVERT: Z 550 LYS cc_start: 0.8672 (tmtt) cc_final: 0.8418 (tptp) REVERT: Z 552 PHE cc_start: 0.7876 (m-80) cc_final: 0.7537 (m-80) REVERT: Z 617 ARG cc_start: 0.8147 (ptm160) cc_final: 0.7875 (ptm160) REVERT: Z 620 ARG cc_start: 0.8125 (mtp180) cc_final: 0.7493 (ptp-170) REVERT: Z 623 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8163 (mm-30) REVERT: Z 624 MET cc_start: 0.7932 (ptp) cc_final: 0.7461 (ptp) REVERT: Z 627 GLN cc_start: 0.8191 (pp30) cc_final: 0.7875 (pp30) REVERT: Z 673 TYR cc_start: 0.7322 (m-10) cc_final: 0.6823 (m-10) REVERT: Z 721 ILE cc_start: 0.7722 (mp) cc_final: 0.7014 (mp) outliers start: 0 outliers final: 0 residues processed: 403 average time/residue: 0.1449 time to fit residues: 84.7554 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 : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 223 optimal weight: 2.9990 chunk 53 optimal weight: 0.0040 chunk 83 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 173 optimal weight: 7.9990 chunk 150 optimal weight: 1.9990 overall best weight: 2.2000 ------------------------------------------------------------------------------- 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 154 GLN ** 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 251 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 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN Y 135 GLN Y 376 ASN ** Y 457 ASN ** 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 8 GLN ** Z 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 757 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.143382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.110634 restraints weight = 52268.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.115216 restraints weight = 37342.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.118847 restraints weight = 28372.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.121722 restraints weight = 22458.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.123985 restraints weight = 18320.986| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3859 r_free = 0.3859 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 18117 Z= 0.194 Angle : 0.763 9.810 24626 Z= 0.399 Chirality : 0.050 0.228 2820 Planarity : 0.006 0.084 3186 Dihedral : 6.368 26.540 2447 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 24.61 Ramachandran Plot: Outliers : 0.27 % Allowed : 13.01 % Favored : 86.72 % Rotamer: Outliers : 0.05 % Allowed : 5.18 % Favored : 94.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.57 (0.16), residues: 2244 helix: -1.00 (0.20), residues: 576 sheet: -2.26 (0.22), residues: 504 loop : -3.22 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 674 TYR 0.026 0.002 TYR X 194 PHE 0.037 0.002 PHE Z 140 TRP 0.040 0.002 TRP Y 262 HIS 0.010 0.002 HIS Y 170 Details of bonding type rmsd covalent geometry : bond 0.00405 (18116) covalent geometry : angle 0.76296 (24626) hydrogen bonds : bond 0.04646 ( 550) hydrogen bonds : angle 6.57927 ( 1524) Misc. bond : bond 0.00075 ( 1) *********************** 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 409 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 408 time to evaluate : 0.520 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 1 MET cc_start: 0.7808 (mmm) cc_final: 0.7565 (mmm) REVERT: X 40 PHE cc_start: 0.7927 (p90) cc_final: 0.7535 (p90) REVERT: X 70 GLN cc_start: 0.7405 (mp10) cc_final: 0.7051 (mp10) REVERT: X 75 ASN cc_start: 0.8335 (p0) cc_final: 0.7774 (p0) REVERT: X 108 ILE cc_start: 0.8408 (mp) cc_final: 0.8140 (mp) REVERT: X 199 MET cc_start: 0.7999 (ppp) cc_final: 0.7604 (ppp) REVERT: X 219 TYR cc_start: 0.8559 (m-80) cc_final: 0.8301 (m-80) REVERT: X 222 ASN cc_start: 0.8931 (m-40) cc_final: 0.8486 (p0) REVERT: X 265 MET cc_start: 0.4741 (mpp) cc_final: 0.4254 (mpp) REVERT: X 303 TYR cc_start: 0.6837 (m-10) cc_final: 0.6402 (m-80) REVERT: X 305 TYR cc_start: 0.7857 (m-10) cc_final: 0.7538 (m-10) REVERT: X 352 TYR cc_start: 0.8422 (m-10) cc_final: 0.8008 (m-10) REVERT: X 356 TRP cc_start: 0.6855 (m100) cc_final: 0.6423 (m100) REVERT: X 375 LEU cc_start: 0.8192 (mm) cc_final: 0.7921 (mm) REVERT: X 385 TYR cc_start: 0.8275 (t80) cc_final: 0.8055 (t80) REVERT: X 394 TRP cc_start: 0.8163 (m-10) cc_final: 0.7769 (m-10) REVERT: X 404 LEU cc_start: 0.8337 (mp) cc_final: 0.7961 (pp) REVERT: X 429 ARG cc_start: 0.9031 (ppt170) cc_final: 0.8804 (ppt170) REVERT: X 491 ARG cc_start: 0.7056 (mtt180) cc_final: 0.6606 (mtt-85) REVERT: X 527 MET cc_start: 0.8565 (mtm) cc_final: 0.7892 (mtm) REVERT: X 531 PHE cc_start: 0.8717 (m-80) cc_final: 0.8171 (m-80) REVERT: X 549 MET cc_start: 0.9244 (mpp) cc_final: 0.8926 (mmm) REVERT: X 550 LYS cc_start: 0.8705 (pttm) cc_final: 0.8256 (pttp) REVERT: X 552 PHE cc_start: 0.9048 (t80) cc_final: 0.7994 (t80) REVERT: X 554 LYS cc_start: 0.9349 (tmtt) cc_final: 0.9061 (tptp) REVERT: X 617 ARG cc_start: 0.8688 (mmt-90) cc_final: 0.8302 (mmt-90) REVERT: X 620 ARG cc_start: 0.9126 (ptm-80) cc_final: 0.8796 (ptm-80) REVERT: X 621 LEU cc_start: 0.9399 (pp) cc_final: 0.9139 (pp) REVERT: X 623 GLU cc_start: 0.8499 (mp0) cc_final: 0.7929 (mm-30) REVERT: X 662 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8713 (pt0) REVERT: X 666 LYS cc_start: 0.8695 (ptmm) cc_final: 0.8361 (pptt) REVERT: X 673 TYR cc_start: 0.8507 (m-80) cc_final: 0.8156 (m-80) REVERT: X 727 LEU cc_start: 0.8969 (mm) cc_final: 0.8766 (mm) REVERT: X 748 ASP cc_start: 0.9045 (t0) cc_final: 0.8653 (t0) REVERT: X 755 PHE cc_start: 0.8621 (m-80) cc_final: 0.7811 (m-10) REVERT: X 764 ARG cc_start: 0.9446 (mtm180) cc_final: 0.9220 (mtm180) REVERT: X 772 MET cc_start: 0.8683 (mtm) cc_final: 0.8082 (mtm) REVERT: X 774 CYS cc_start: 0.7472 (p) cc_final: 0.7116 (p) REVERT: X 775 ARG cc_start: 0.8422 (tmt170) cc_final: 0.7839 (tmt170) REVERT: Y 94 GLU cc_start: 0.8325 (tt0) cc_final: 0.7000 (tm-30) REVERT: Y 116 ASN cc_start: 0.8107 (m-40) cc_final: 0.7683 (t0) REVERT: Y 128 LEU cc_start: 0.7851 (tt) cc_final: 0.7180 (pp) REVERT: Y 142 ASP cc_start: 0.7434 (t0) cc_final: 0.6813 (t0) REVERT: Y 155 TYR cc_start: 0.7890 (m-10) cc_final: 0.7509 (m-10) REVERT: Y 208 ILE cc_start: 0.8933 (mm) cc_final: 0.8535 (tt) REVERT: Y 213 GLU cc_start: 0.7897 (mt-10) cc_final: 0.6946 (mm-30) REVERT: Y 216 CYS cc_start: 0.9363 (t) cc_final: 0.9027 (t) REVERT: Y 263 LYS cc_start: 0.7694 (mmmt) cc_final: 0.7450 (tppt) REVERT: Y 265 MET cc_start: 0.7812 (mmp) cc_final: 0.7019 (mmm) REVERT: Y 275 PHE cc_start: 0.7054 (t80) cc_final: 0.6845 (t80) REVERT: Y 277 PHE cc_start: 0.7328 (t80) cc_final: 0.7068 (t80) REVERT: Y 297 LYS cc_start: 0.8325 (mmpt) cc_final: 0.7838 (mmtm) REVERT: Y 405 HIS cc_start: 0.8257 (p90) cc_final: 0.8025 (p90) REVERT: Y 434 GLU cc_start: 0.8199 (pm20) cc_final: 0.7987 (mm-30) REVERT: Y 444 LEU cc_start: 0.9130 (tp) cc_final: 0.8588 (pp) REVERT: Y 450 LEU cc_start: 0.8814 (mt) cc_final: 0.8541 (tp) REVERT: Y 505 PHE cc_start: 0.9007 (m-10) cc_final: 0.8603 (m-80) REVERT: Y 520 LEU cc_start: 0.8708 (tp) cc_final: 0.8073 (mp) REVERT: Y 591 TRP cc_start: 0.8539 (m-90) cc_final: 0.7520 (m-90) REVERT: Y 617 ARG cc_start: 0.8712 (tpm170) cc_final: 0.8441 (tpm170) REVERT: Y 649 THR cc_start: 0.7899 (t) cc_final: 0.7058 (p) REVERT: Y 650 GLN cc_start: 0.8915 (mm110) cc_final: 0.8703 (pm20) REVERT: Y 682 PHE cc_start: 0.8460 (m-80) cc_final: 0.8018 (m-80) REVERT: Y 762 ILE cc_start: 0.8537 (pt) cc_final: 0.8166 (pt) REVERT: Y 772 MET cc_start: 0.9006 (mmp) cc_final: 0.8753 (mmp) REVERT: Z 11 THR cc_start: 0.8672 (m) cc_final: 0.7533 (m) REVERT: Z 14 TYR cc_start: 0.8111 (p90) cc_final: 0.7243 (p90) REVERT: Z 82 MET cc_start: 0.6307 (mpp) cc_final: 0.5300 (mpp) REVERT: Z 94 GLU cc_start: 0.7827 (mp0) cc_final: 0.7570 (mp0) REVERT: Z 189 TYR cc_start: 0.9383 (m-10) cc_final: 0.9036 (m-10) REVERT: Z 199 MET cc_start: 0.8809 (mmp) cc_final: 0.8563 (mmp) REVERT: Z 212 GLU cc_start: 0.8892 (mp0) cc_final: 0.8623 (mp0) REVERT: Z 215 LYS cc_start: 0.7526 (mppt) cc_final: 0.7020 (mmtt) REVERT: Z 219 TYR cc_start: 0.7831 (m-10) cc_final: 0.7356 (m-80) REVERT: Z 267 TYR cc_start: 0.8138 (m-80) cc_final: 0.7761 (m-80) REVERT: Z 276 LYS cc_start: 0.7442 (ptpt) cc_final: 0.6918 (tmmt) REVERT: Z 301 TYR cc_start: 0.8379 (m-10) cc_final: 0.7084 (m-10) REVERT: Z 302 GLN cc_start: 0.8204 (mp10) cc_final: 0.7527 (mm-40) REVERT: Z 421 LEU cc_start: 0.8694 (mt) cc_final: 0.8360 (mt) REVERT: Z 477 ASN cc_start: 0.8428 (t0) cc_final: 0.8197 (t0) REVERT: Z 479 ASP cc_start: 0.9074 (m-30) cc_final: 0.8418 (m-30) REVERT: Z 500 GLU cc_start: 0.8761 (pp20) cc_final: 0.8422 (pp20) REVERT: Z 501 LEU cc_start: 0.8641 (mt) cc_final: 0.8410 (mt) REVERT: Z 530 MET cc_start: 0.8957 (tpt) cc_final: 0.8602 (tpp) REVERT: Z 549 MET cc_start: 0.8843 (ppp) cc_final: 0.8308 (ppp) REVERT: Z 551 LYS cc_start: 0.7751 (ptpt) cc_final: 0.7464 (ptpt) REVERT: Z 591 TRP cc_start: 0.6852 (m-10) cc_final: 0.6627 (m-10) REVERT: Z 617 ARG cc_start: 0.8034 (ptm160) cc_final: 0.7640 (ptm160) REVERT: Z 623 GLU cc_start: 0.8849 (mm-30) cc_final: 0.7941 (mm-30) REVERT: Z 624 MET cc_start: 0.8087 (ptp) cc_final: 0.7636 (ptp) REVERT: Z 627 GLN cc_start: 0.7954 (pp30) cc_final: 0.7280 (pp30) REVERT: Z 673 TYR cc_start: 0.7690 (m-10) cc_final: 0.6996 (m-10) REVERT: Z 721 ILE cc_start: 0.7813 (mp) cc_final: 0.7152 (mp) outliers start: 1 outliers final: 1 residues processed: 409 average time/residue: 0.1424 time to fit residues: 84.9000 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 : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 199 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 187 optimal weight: 0.0970 chunk 33 optimal weight: 0.2980 chunk 42 optimal weight: 9.9990 chunk 186 optimal weight: 4.9990 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 180 GLN X 188 HIS ** X 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 315 HIS ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 457 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 456 ASN Z 677 ASN Z 757 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.148316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.116068 restraints weight = 51914.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.120872 restraints weight = 36693.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.124577 restraints weight = 27642.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.127574 restraints weight = 21783.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.129895 restraints weight = 17642.422| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3929 r_free = 0.3929 target_work(ls_wunit_k1) = 0.129 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18117 Z= 0.138 Angle : 0.746 10.466 24626 Z= 0.380 Chirality : 0.049 0.236 2820 Planarity : 0.006 0.078 3186 Dihedral : 6.112 28.258 2447 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 10.61 % Favored : 89.13 % Rotamer: Outliers : 0.05 % Allowed : 3.74 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.49 (0.16), residues: 2244 helix: -0.91 (0.20), residues: 571 sheet: -2.25 (0.22), residues: 498 loop : -3.16 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG Y 274 TYR 0.018 0.002 TYR Y 45 PHE 0.033 0.002 PHE Z 140 TRP 0.030 0.002 TRP Y 262 HIS 0.013 0.002 HIS Y 170 Details of bonding type rmsd covalent geometry : bond 0.00307 (18116) covalent geometry : angle 0.74630 (24626) hydrogen bonds : bond 0.03923 ( 550) hydrogen bonds : angle 6.16442 ( 1524) Misc. bond : bond 0.00060 ( 1) *********************** 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 411 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 410 time to evaluate : 0.462 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 40 PHE cc_start: 0.7946 (p90) cc_final: 0.7330 (p90) REVERT: X 74 PHE cc_start: 0.9191 (t80) cc_final: 0.8782 (t80) REVERT: X 75 ASN cc_start: 0.8278 (p0) cc_final: 0.7656 (p0) REVERT: X 194 TYR cc_start: 0.7737 (m-10) cc_final: 0.7459 (m-10) REVERT: X 199 MET cc_start: 0.7875 (ppp) cc_final: 0.7557 (ppp) REVERT: X 215 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7805 (mtmm) REVERT: X 219 TYR cc_start: 0.8513 (m-80) cc_final: 0.8187 (m-80) REVERT: X 222 ASN cc_start: 0.8882 (m-40) cc_final: 0.8428 (p0) REVERT: X 265 MET cc_start: 0.4559 (mpp) cc_final: 0.4324 (mpp) REVERT: X 305 TYR cc_start: 0.7609 (m-10) cc_final: 0.6946 (m-10) REVERT: X 347 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8337 (mm-30) REVERT: X 356 TRP cc_start: 0.6789 (m100) cc_final: 0.6359 (m100) REVERT: X 375 LEU cc_start: 0.8217 (mm) cc_final: 0.7957 (mm) REVERT: X 385 TYR cc_start: 0.8253 (t80) cc_final: 0.8015 (t80) REVERT: X 393 GLN cc_start: 0.8844 (mp10) cc_final: 0.8027 (tp-100) REVERT: X 394 TRP cc_start: 0.8077 (m-10) cc_final: 0.7728 (m-10) REVERT: X 404 LEU cc_start: 0.8192 (mp) cc_final: 0.7926 (pp) REVERT: X 413 THR cc_start: 0.8885 (m) cc_final: 0.8629 (t) REVERT: X 414 GLN cc_start: 0.8211 (tp-100) cc_final: 0.7215 (tp40) REVERT: X 429 ARG cc_start: 0.9088 (ppt170) cc_final: 0.8817 (ppt170) REVERT: X 491 ARG cc_start: 0.7085 (mtt180) cc_final: 0.6672 (mtt-85) REVERT: X 527 MET cc_start: 0.8406 (mtm) cc_final: 0.7649 (mtm) REVERT: X 531 PHE cc_start: 0.8677 (m-80) cc_final: 0.8225 (m-80) REVERT: X 544 MET cc_start: 0.8171 (mmp) cc_final: 0.7955 (mmp) REVERT: X 549 MET cc_start: 0.9233 (mpp) cc_final: 0.8858 (mmm) REVERT: X 552 PHE cc_start: 0.8944 (t80) cc_final: 0.7929 (t80) REVERT: X 554 LYS cc_start: 0.9314 (tmtt) cc_final: 0.9012 (tptp) REVERT: X 617 ARG cc_start: 0.8620 (mmt-90) cc_final: 0.8239 (mmt-90) REVERT: X 620 ARG cc_start: 0.9092 (ptm-80) cc_final: 0.8686 (ptm-80) REVERT: X 621 LEU cc_start: 0.9267 (pp) cc_final: 0.9040 (pp) REVERT: X 623 GLU cc_start: 0.8462 (mp0) cc_final: 0.7676 (mm-30) REVERT: X 662 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8642 (pt0) REVERT: X 666 LYS cc_start: 0.8616 (ptmm) cc_final: 0.8168 (tptp) REVERT: X 673 TYR cc_start: 0.8516 (m-80) cc_final: 0.8260 (m-80) REVERT: X 698 PHE cc_start: 0.8737 (p90) cc_final: 0.8517 (p90) REVERT: X 727 LEU cc_start: 0.8931 (mm) cc_final: 0.8698 (mm) REVERT: X 748 ASP cc_start: 0.8916 (t0) cc_final: 0.8566 (t0) REVERT: X 772 MET cc_start: 0.8690 (mtm) cc_final: 0.8157 (mtm) REVERT: Y 1 MET cc_start: 0.7008 (tpt) cc_final: 0.6762 (tpt) REVERT: Y 94 GLU cc_start: 0.8236 (tt0) cc_final: 0.6994 (tm-30) REVERT: Y 116 ASN cc_start: 0.7997 (m-40) cc_final: 0.7542 (t0) REVERT: Y 128 LEU cc_start: 0.7853 (tt) cc_final: 0.7242 (pp) REVERT: Y 142 ASP cc_start: 0.7265 (t0) cc_final: 0.6627 (t0) REVERT: Y 155 TYR cc_start: 0.7598 (m-10) cc_final: 0.7241 (m-10) REVERT: Y 170 HIS cc_start: 0.8207 (t70) cc_final: 0.7664 (t70) REVERT: Y 216 CYS cc_start: 0.9266 (t) cc_final: 0.9025 (t) REVERT: Y 246 TYR cc_start: 0.6941 (t80) cc_final: 0.6336 (t80) REVERT: Y 277 PHE cc_start: 0.7395 (t80) cc_final: 0.7078 (t80) REVERT: Y 297 LYS cc_start: 0.8320 (mmpt) cc_final: 0.7865 (mmtm) REVERT: Y 338 VAL cc_start: 0.8440 (p) cc_final: 0.8143 (m) REVERT: Y 434 GLU cc_start: 0.8214 (pm20) cc_final: 0.8004 (mm-30) REVERT: Y 444 LEU cc_start: 0.9118 (tp) cc_final: 0.8510 (pp) REVERT: Y 491 ARG cc_start: 0.8508 (mmp-170) cc_final: 0.8306 (mmp-170) REVERT: Y 505 PHE cc_start: 0.8876 (m-10) cc_final: 0.8460 (m-10) REVERT: Y 530 MET cc_start: 0.8154 (tpt) cc_final: 0.7921 (tmm) REVERT: Y 539 ASP cc_start: 0.7074 (t0) cc_final: 0.6847 (t0) REVERT: Y 591 TRP cc_start: 0.8434 (m-90) cc_final: 0.7624 (m-90) REVERT: Y 617 ARG cc_start: 0.8659 (tpm170) cc_final: 0.8372 (tpm170) REVERT: Y 618 ARG cc_start: 0.9419 (mtp180) cc_final: 0.9124 (ttm170) REVERT: Y 649 THR cc_start: 0.7947 (t) cc_final: 0.7183 (p) REVERT: Y 682 PHE cc_start: 0.8414 (m-80) cc_final: 0.8189 (m-80) REVERT: Y 718 ILE cc_start: 0.8461 (mm) cc_final: 0.8180 (mm) REVERT: Y 762 ILE cc_start: 0.8431 (pt) cc_final: 0.8041 (pt) REVERT: Y 772 MET cc_start: 0.9004 (mmp) cc_final: 0.8797 (mmp) REVERT: Z 14 TYR cc_start: 0.7946 (p90) cc_final: 0.6974 (p90) REVERT: Z 189 TYR cc_start: 0.9390 (m-10) cc_final: 0.9002 (m-10) REVERT: Z 199 MET cc_start: 0.8705 (mmp) cc_final: 0.8041 (tmm) REVERT: Z 212 GLU cc_start: 0.8825 (mp0) cc_final: 0.8553 (mp0) REVERT: Z 215 LYS cc_start: 0.7605 (mppt) cc_final: 0.7145 (mttm) REVERT: Z 219 TYR cc_start: 0.7792 (m-10) cc_final: 0.7304 (m-80) REVERT: Z 265 MET cc_start: 0.7511 (mpp) cc_final: 0.6364 (mpp) REVERT: Z 267 TYR cc_start: 0.8091 (m-80) cc_final: 0.7276 (m-80) REVERT: Z 342 PHE cc_start: 0.6910 (t80) cc_final: 0.6660 (t80) REVERT: Z 346 LYS cc_start: 0.8137 (ptmm) cc_final: 0.7928 (ttpp) REVERT: Z 500 GLU cc_start: 0.8663 (pp20) cc_final: 0.8182 (pp20) REVERT: Z 501 LEU cc_start: 0.8603 (mt) cc_final: 0.8295 (mt) REVERT: Z 514 MET cc_start: 0.7263 (tmm) cc_final: 0.7008 (tmm) REVERT: Z 530 MET cc_start: 0.8954 (tpt) cc_final: 0.8573 (tpp) REVERT: Z 549 MET cc_start: 0.8616 (ppp) cc_final: 0.8017 (ppp) REVERT: Z 550 LYS cc_start: 0.8615 (tmtt) cc_final: 0.8391 (tptp) REVERT: Z 617 ARG cc_start: 0.8044 (ptm160) cc_final: 0.7636 (ptm160) REVERT: Z 623 GLU cc_start: 0.8771 (mm-30) cc_final: 0.7753 (mm-30) REVERT: Z 624 MET cc_start: 0.8021 (ptp) cc_final: 0.7588 (ptp) REVERT: Z 627 GLN cc_start: 0.7886 (pp30) cc_final: 0.7173 (pp30) REVERT: Z 673 TYR cc_start: 0.7518 (m-10) cc_final: 0.6804 (m-10) REVERT: Z 721 ILE cc_start: 0.7868 (mp) cc_final: 0.7151 (mp) outliers start: 1 outliers final: 1 residues processed: 411 average time/residue: 0.1326 time to fit residues: 79.5585 Evaluate side-chains 359 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 154 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 212 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 251 ASN ** 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** X 760 ASN Y 97 ASN ** Y 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 632 ASN ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 456 ASN ** Z 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 739 GLN Z 757 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.144388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111324 restraints weight = 55787.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.115929 restraints weight = 40585.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.119492 restraints weight = 31249.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.122253 restraints weight = 24995.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.124573 restraints weight = 20629.040| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3861 r_free = 0.3861 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3861 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 18117 Z= 0.175 Angle : 0.762 10.578 24626 Z= 0.392 Chirality : 0.050 0.221 2820 Planarity : 0.006 0.084 3186 Dihedral : 6.241 32.369 2447 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 23.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 12.70 % Favored : 87.08 % Rotamer: Outliers : 0.05 % Allowed : 3.24 % Favored : 96.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.51 (0.16), residues: 2244 helix: -0.89 (0.21), residues: 572 sheet: -2.33 (0.22), residues: 480 loop : -3.16 (0.17), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 427 TYR 0.016 0.002 TYR X 303 PHE 0.025 0.002 PHE Z 140 TRP 0.038 0.002 TRP Y 262 HIS 0.011 0.002 HIS X 315 Details of bonding type rmsd covalent geometry : bond 0.00376 (18116) covalent geometry : angle 0.76223 (24626) hydrogen bonds : bond 0.04161 ( 550) hydrogen bonds : angle 6.32000 ( 1524) Misc. bond : bond 0.00065 ( 1) *********************** 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 401 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 400 time to evaluate : 0.588 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 40 PHE cc_start: 0.7806 (p90) cc_final: 0.7257 (p90) REVERT: X 74 PHE cc_start: 0.9159 (t80) cc_final: 0.8917 (t80) REVERT: X 75 ASN cc_start: 0.8323 (p0) cc_final: 0.7674 (p0) REVERT: X 199 MET cc_start: 0.7897 (ppp) cc_final: 0.7540 (ppp) REVERT: X 215 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8018 (mtmm) REVERT: X 219 TYR cc_start: 0.8521 (m-80) cc_final: 0.8181 (m-80) REVERT: X 222 ASN cc_start: 0.8803 (m-40) cc_final: 0.8385 (p0) REVERT: X 347 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8281 (mm-30) REVERT: X 356 TRP cc_start: 0.6845 (m100) cc_final: 0.6452 (m100) REVERT: X 375 LEU cc_start: 0.8222 (mm) cc_final: 0.7983 (mm) REVERT: X 385 TYR cc_start: 0.8395 (t80) cc_final: 0.8130 (t80) REVERT: X 393 GLN cc_start: 0.8739 (mp10) cc_final: 0.7919 (tp-100) REVERT: X 394 TRP cc_start: 0.8168 (m-10) cc_final: 0.7696 (m-10) REVERT: X 413 THR cc_start: 0.8923 (m) cc_final: 0.8712 (t) REVERT: X 491 ARG cc_start: 0.7229 (mtt180) cc_final: 0.6808 (mtt-85) REVERT: X 527 MET cc_start: 0.8431 (mtm) cc_final: 0.7348 (mtm) REVERT: X 544 MET cc_start: 0.8106 (mmp) cc_final: 0.7754 (mmp) REVERT: X 549 MET cc_start: 0.9203 (mpp) cc_final: 0.8819 (mmm) REVERT: X 552 PHE cc_start: 0.8952 (t80) cc_final: 0.7999 (t80) REVERT: X 554 LYS cc_start: 0.9343 (tmtt) cc_final: 0.9041 (tptp) REVERT: X 617 ARG cc_start: 0.8598 (mmt-90) cc_final: 0.8223 (mmt-90) REVERT: X 620 ARG cc_start: 0.9059 (ptm-80) cc_final: 0.8659 (ptm-80) REVERT: X 621 LEU cc_start: 0.9357 (pp) cc_final: 0.9131 (pp) REVERT: X 623 GLU cc_start: 0.8516 (mp0) cc_final: 0.7760 (mt-10) REVERT: X 662 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8550 (pt0) REVERT: X 673 TYR cc_start: 0.8511 (m-80) cc_final: 0.8155 (m-80) REVERT: X 698 PHE cc_start: 0.8815 (p90) cc_final: 0.8577 (p90) REVERT: X 727 LEU cc_start: 0.8938 (mm) cc_final: 0.8719 (mm) REVERT: X 748 ASP cc_start: 0.8858 (t0) cc_final: 0.8536 (t0) REVERT: X 760 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7919 (p0) REVERT: X 772 MET cc_start: 0.8712 (mtm) cc_final: 0.8171 (mtm) REVERT: Y 64 LEU cc_start: 0.9209 (pp) cc_final: 0.8845 (pp) REVERT: Y 94 GLU cc_start: 0.8290 (tt0) cc_final: 0.7083 (tm-30) REVERT: Y 116 ASN cc_start: 0.8075 (m-40) cc_final: 0.7627 (t0) REVERT: Y 128 LEU cc_start: 0.7766 (tt) cc_final: 0.7112 (pp) REVERT: Y 142 ASP cc_start: 0.7271 (t0) cc_final: 0.6643 (t0) REVERT: Y 155 TYR cc_start: 0.7632 (m-10) cc_final: 0.7356 (m-10) REVERT: Y 170 HIS cc_start: 0.8007 (t70) cc_final: 0.7422 (t70) REVERT: Y 208 ILE cc_start: 0.8971 (mm) cc_final: 0.8577 (mm) REVERT: Y 215 LYS cc_start: 0.9141 (tttt) cc_final: 0.8877 (tttt) REVERT: Y 275 PHE cc_start: 0.7352 (t80) cc_final: 0.6922 (t80) REVERT: Y 277 PHE cc_start: 0.7451 (t80) cc_final: 0.7037 (t80) REVERT: Y 297 LYS cc_start: 0.8329 (mmpt) cc_final: 0.7832 (mmtm) REVERT: Y 338 VAL cc_start: 0.8421 (p) cc_final: 0.8123 (m) REVERT: Y 344 VAL cc_start: 0.7836 (t) cc_final: 0.7503 (t) REVERT: Y 444 LEU cc_start: 0.9109 (tp) cc_final: 0.8535 (pp) REVERT: Y 505 PHE cc_start: 0.8877 (m-10) cc_final: 0.8382 (m-10) REVERT: Y 552 PHE cc_start: 0.7238 (t80) cc_final: 0.7029 (t80) REVERT: Y 591 TRP cc_start: 0.8552 (m-90) cc_final: 0.7752 (m-90) REVERT: Y 617 ARG cc_start: 0.8727 (tpm170) cc_final: 0.8394 (tpm170) REVERT: Y 618 ARG cc_start: 0.9492 (mtp180) cc_final: 0.9231 (ttm170) REVERT: Y 649 THR cc_start: 0.7672 (t) cc_final: 0.7221 (p) REVERT: Y 682 PHE cc_start: 0.8386 (m-80) cc_final: 0.7716 (m-80) REVERT: Y 718 ILE cc_start: 0.8493 (mm) cc_final: 0.8178 (mm) REVERT: Y 774 CYS cc_start: 0.6577 (p) cc_final: 0.6362 (p) REVERT: Z 11 THR cc_start: 0.8526 (m) cc_final: 0.7288 (m) REVERT: Z 14 TYR cc_start: 0.8089 (p90) cc_final: 0.7307 (p90) REVERT: Z 189 TYR cc_start: 0.9439 (m-10) cc_final: 0.9086 (m-10) REVERT: Z 199 MET cc_start: 0.8655 (mmp) cc_final: 0.8452 (tpp) REVERT: Z 219 TYR cc_start: 0.7763 (m-10) cc_final: 0.7320 (m-80) REVERT: Z 267 TYR cc_start: 0.8190 (m-80) cc_final: 0.7349 (m-80) REVERT: Z 294 ILE cc_start: 0.7023 (tp) cc_final: 0.6803 (tp) REVERT: Z 356 TRP cc_start: 0.6705 (m100) cc_final: 0.5752 (m100) REVERT: Z 500 GLU cc_start: 0.8789 (pp20) cc_final: 0.8331 (pp20) REVERT: Z 501 LEU cc_start: 0.8705 (mt) cc_final: 0.8379 (mt) REVERT: Z 530 MET cc_start: 0.8957 (tpt) cc_final: 0.8535 (tpp) REVERT: Z 549 MET cc_start: 0.8689 (ppp) cc_final: 0.7608 (ppp) REVERT: Z 550 LYS cc_start: 0.8650 (tmtt) cc_final: 0.8268 (mmtp) REVERT: Z 551 LYS cc_start: 0.7770 (ptpp) cc_final: 0.7475 (ptpp) REVERT: Z 591 TRP cc_start: 0.7254 (m-10) cc_final: 0.6973 (m-10) REVERT: Z 617 ARG cc_start: 0.8084 (ptm160) cc_final: 0.7733 (ptm160) REVERT: Z 622 LYS cc_start: 0.8710 (mmpt) cc_final: 0.8363 (mmpt) REVERT: Z 623 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8129 (mm-30) REVERT: Z 624 MET cc_start: 0.8203 (ptp) cc_final: 0.7765 (ptp) REVERT: Z 627 GLN cc_start: 0.7883 (pp30) cc_final: 0.7233 (pp30) REVERT: Z 629 GLU cc_start: 0.7454 (mp0) cc_final: 0.6993 (mp0) REVERT: Z 673 TYR cc_start: 0.7724 (m-10) cc_final: 0.7267 (m-10) REVERT: Z 721 ILE cc_start: 0.7974 (mp) cc_final: 0.7274 (mp) outliers start: 1 outliers final: 0 residues processed: 401 average time/residue: 0.1309 time to fit residues: 76.7710 Evaluate side-chains 353 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 109 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 86 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 113 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 189 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 44 optimal weight: 0.0040 overall best weight: 0.9794 ------------------------------------------------------------------------------- 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 251 ASN X 315 HIS ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN ** Y 405 HIS ** 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 279 ASN ** Z 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 757 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.147276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.114658 restraints weight = 56851.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.119383 restraints weight = 40960.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.123041 restraints weight = 31240.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.125980 restraints weight = 24795.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.128291 restraints weight = 20270.378| |-----------------------------------------------------------------------------| r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3907 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3907 r_free = 0.3907 target_work(ls_wunit_k1) = 0.127 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3907 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18117 Z= 0.138 Angle : 0.756 10.358 24626 Z= 0.384 Chirality : 0.050 0.262 2820 Planarity : 0.006 0.079 3186 Dihedral : 6.054 31.432 2447 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.05 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.50 (0.16), residues: 2244 helix: -0.84 (0.21), residues: 572 sheet: -2.36 (0.21), residues: 500 loop : -3.16 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 753 TYR 0.020 0.001 TYR Z 301 PHE 0.025 0.002 PHE Z 140 TRP 0.027 0.002 TRP Y 262 HIS 0.010 0.002 HIS Y 170 Details of bonding type rmsd covalent geometry : bond 0.00308 (18116) covalent geometry : angle 0.75635 (24626) hydrogen bonds : bond 0.03795 ( 550) hydrogen bonds : angle 6.11506 ( 1524) Misc. bond : bond 0.00053 ( 1) *********************** 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 402 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.427 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 18 LEU cc_start: 0.8411 (mt) cc_final: 0.8185 (mt) REVERT: X 40 PHE cc_start: 0.7767 (p90) cc_final: 0.7206 (p90) REVERT: X 74 PHE cc_start: 0.9153 (t80) cc_final: 0.8884 (t80) REVERT: X 75 ASN cc_start: 0.8304 (p0) cc_final: 0.7662 (p0) REVERT: X 194 TYR cc_start: 0.7480 (m-10) cc_final: 0.7141 (m-10) REVERT: X 199 MET cc_start: 0.7689 (ppp) cc_final: 0.7381 (ppp) REVERT: X 215 LYS cc_start: 0.8286 (mtmm) cc_final: 0.7980 (mtmm) REVERT: X 219 TYR cc_start: 0.8540 (m-80) cc_final: 0.8229 (m-80) REVERT: X 222 ASN cc_start: 0.8801 (m-40) cc_final: 0.8365 (p0) REVERT: X 265 MET cc_start: 0.4306 (mpp) cc_final: 0.4024 (mpp) REVERT: X 317 THR cc_start: 0.6027 (m) cc_final: 0.5564 (m) REVERT: X 347 GLU cc_start: 0.8853 (mt-10) cc_final: 0.8257 (mm-30) REVERT: X 356 TRP cc_start: 0.6886 (m100) cc_final: 0.6533 (m100) REVERT: X 375 LEU cc_start: 0.8170 (mm) cc_final: 0.7915 (mm) REVERT: X 385 TYR cc_start: 0.8318 (t80) cc_final: 0.8010 (t80) REVERT: X 393 GLN cc_start: 0.8728 (mp10) cc_final: 0.7912 (tp-100) REVERT: X 413 THR cc_start: 0.8937 (m) cc_final: 0.8710 (t) REVERT: X 491 ARG cc_start: 0.7312 (mtt180) cc_final: 0.6982 (mtt-85) REVERT: X 527 MET cc_start: 0.8554 (mtm) cc_final: 0.7239 (mtm) REVERT: X 544 MET cc_start: 0.8102 (mmp) cc_final: 0.7756 (mmp) REVERT: X 549 MET cc_start: 0.9177 (mpp) cc_final: 0.8809 (mmt) REVERT: X 552 PHE cc_start: 0.9010 (t80) cc_final: 0.8043 (t80) REVERT: X 554 LYS cc_start: 0.9332 (tmtt) cc_final: 0.9034 (tptp) REVERT: X 617 ARG cc_start: 0.8531 (mmt-90) cc_final: 0.8264 (mmt-90) REVERT: X 623 GLU cc_start: 0.8329 (mp0) cc_final: 0.7629 (mm-30) REVERT: X 662 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8457 (pt0) REVERT: X 673 TYR cc_start: 0.8561 (m-80) cc_final: 0.8171 (m-80) REVERT: X 698 PHE cc_start: 0.8885 (p90) cc_final: 0.8629 (p90) REVERT: X 738 LYS cc_start: 0.8348 (mmpt) cc_final: 0.8143 (mmmt) REVERT: X 748 ASP cc_start: 0.8770 (t0) cc_final: 0.8400 (t0) REVERT: X 772 MET cc_start: 0.8705 (mtm) cc_final: 0.8161 (mtm) REVERT: Y 1 MET cc_start: 0.7396 (tpt) cc_final: 0.7175 (tpt) REVERT: Y 64 LEU cc_start: 0.9177 (pp) cc_final: 0.8852 (pp) REVERT: Y 94 GLU cc_start: 0.8267 (tt0) cc_final: 0.7068 (tm-30) REVERT: Y 116 ASN cc_start: 0.8086 (m-40) cc_final: 0.7645 (t0) REVERT: Y 128 LEU cc_start: 0.7737 (tt) cc_final: 0.7106 (pp) REVERT: Y 142 ASP cc_start: 0.7268 (t0) cc_final: 0.6470 (t0) REVERT: Y 155 TYR cc_start: 0.7614 (m-10) cc_final: 0.7233 (m-10) REVERT: Y 170 HIS cc_start: 0.7890 (t70) cc_final: 0.7286 (t70) REVERT: Y 208 ILE cc_start: 0.8842 (mm) cc_final: 0.8578 (mm) REVERT: Y 215 LYS cc_start: 0.9059 (tttt) cc_final: 0.8816 (tttt) REVERT: Y 265 MET cc_start: 0.7395 (tpt) cc_final: 0.7058 (tpt) REVERT: Y 275 PHE cc_start: 0.7313 (t80) cc_final: 0.6878 (t80) REVERT: Y 277 PHE cc_start: 0.7502 (t80) cc_final: 0.7048 (t80) REVERT: Y 297 LYS cc_start: 0.8257 (mmpt) cc_final: 0.7714 (mmtm) REVERT: Y 338 VAL cc_start: 0.8403 (p) cc_final: 0.8133 (m) REVERT: Y 434 GLU cc_start: 0.8161 (pm20) cc_final: 0.7900 (mm-30) REVERT: Y 444 LEU cc_start: 0.9163 (tp) cc_final: 0.8546 (pp) REVERT: Y 505 PHE cc_start: 0.8890 (m-10) cc_final: 0.8525 (m-10) REVERT: Y 591 TRP cc_start: 0.8513 (m-90) cc_final: 0.7312 (m-90) REVERT: Y 617 ARG cc_start: 0.8668 (tpm170) cc_final: 0.8394 (tpm170) REVERT: Y 649 THR cc_start: 0.7925 (t) cc_final: 0.7553 (p) REVERT: Y 718 ILE cc_start: 0.8434 (mm) cc_final: 0.8125 (mm) REVERT: Y 729 ASN cc_start: 0.8459 (m-40) cc_final: 0.8196 (t0) REVERT: Y 762 ILE cc_start: 0.8154 (pt) cc_final: 0.7528 (pt) REVERT: Z 14 TYR cc_start: 0.8019 (p90) cc_final: 0.7040 (p90) REVERT: Z 82 MET cc_start: 0.6249 (mpp) cc_final: 0.5914 (mpp) REVERT: Z 189 TYR cc_start: 0.9459 (m-10) cc_final: 0.9108 (m-10) REVERT: Z 219 TYR cc_start: 0.7671 (m-10) cc_final: 0.7243 (m-80) REVERT: Z 263 LYS cc_start: 0.8595 (ptmm) cc_final: 0.8369 (ptmm) REVERT: Z 265 MET cc_start: 0.7310 (mpp) cc_final: 0.6789 (mpp) REVERT: Z 267 TYR cc_start: 0.8179 (m-80) cc_final: 0.7531 (m-80) REVERT: Z 356 TRP cc_start: 0.6626 (m100) cc_final: 0.5664 (m100) REVERT: Z 500 GLU cc_start: 0.8757 (pp20) cc_final: 0.8493 (pp20) REVERT: Z 530 MET cc_start: 0.8978 (tpt) cc_final: 0.8602 (tpp) REVERT: Z 549 MET cc_start: 0.8496 (ppp) cc_final: 0.8081 (ppp) REVERT: Z 591 TRP cc_start: 0.7276 (m-10) cc_final: 0.6954 (m-10) REVERT: Z 617 ARG cc_start: 0.8024 (ptm160) cc_final: 0.7725 (ptm160) REVERT: Z 622 LYS cc_start: 0.8781 (mmpt) cc_final: 0.8365 (mmpt) REVERT: Z 623 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8006 (mm-30) REVERT: Z 624 MET cc_start: 0.8098 (ptp) cc_final: 0.7704 (ptp) REVERT: Z 627 GLN cc_start: 0.7821 (pp30) cc_final: 0.7138 (pp30) REVERT: Z 673 TYR cc_start: 0.7579 (m-10) cc_final: 0.7196 (m-10) REVERT: Z 721 ILE cc_start: 0.7938 (mp) cc_final: 0.7226 (mp) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.1290 time to fit residues: 75.5098 Evaluate side-chains 360 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 149 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 177 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 188 HIS X 193 ASN X 324 ASN ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN ** Y 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 757 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.146795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.113058 restraints weight = 56674.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.117693 restraints weight = 41411.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.121343 restraints weight = 32036.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.124245 restraints weight = 25714.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.126562 restraints weight = 21223.513| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3886 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3886 r_free = 0.3886 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 18117 Z= 0.151 Angle : 0.766 10.139 24626 Z= 0.390 Chirality : 0.050 0.230 2820 Planarity : 0.006 0.079 3186 Dihedral : 6.055 30.663 2447 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 21.40 Ramachandran Plot: Outliers : 0.22 % Allowed : 11.76 % Favored : 88.01 % Rotamer: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.16), residues: 2244 helix: -0.88 (0.21), residues: 576 sheet: -2.42 (0.21), residues: 498 loop : -3.15 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Y 429 TYR 0.019 0.001 TYR X 303 PHE 0.024 0.002 PHE Z 428 TRP 0.043 0.002 TRP Z 81 HIS 0.010 0.002 HIS Y 170 Details of bonding type rmsd covalent geometry : bond 0.00338 (18116) covalent geometry : angle 0.76583 (24626) hydrogen bonds : bond 0.03877 ( 550) hydrogen bonds : angle 6.17539 ( 1524) Misc. bond : bond 0.00058 ( 1) *********************** 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 413 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.628 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: X 18 LEU cc_start: 0.8468 (mt) cc_final: 0.8257 (mt) REVERT: X 40 PHE cc_start: 0.7858 (p90) cc_final: 0.7310 (p90) REVERT: X 74 PHE cc_start: 0.9159 (t80) cc_final: 0.8877 (t80) REVERT: X 75 ASN cc_start: 0.8202 (p0) cc_final: 0.7520 (p0) REVERT: X 194 TYR cc_start: 0.7401 (m-10) cc_final: 0.7141 (m-10) REVERT: X 199 MET cc_start: 0.7654 (ppp) cc_final: 0.7324 (ppp) REVERT: X 215 LYS cc_start: 0.8273 (mtmm) cc_final: 0.8024 (mtmm) REVERT: X 219 TYR cc_start: 0.8541 (m-80) cc_final: 0.8238 (m-80) REVERT: X 222 ASN cc_start: 0.8818 (m-40) cc_final: 0.8375 (p0) REVERT: X 265 MET cc_start: 0.4343 (mpp) cc_final: 0.4110 (mpp) REVERT: X 305 TYR cc_start: 0.7750 (m-10) cc_final: 0.7399 (m-10) REVERT: X 317 THR cc_start: 0.6109 (m) cc_final: 0.5754 (p) REVERT: X 347 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8503 (mm-30) REVERT: X 356 TRP cc_start: 0.6845 (m100) cc_final: 0.6367 (m100) REVERT: X 375 LEU cc_start: 0.8178 (mm) cc_final: 0.7895 (mm) REVERT: X 385 TYR cc_start: 0.8391 (t80) cc_final: 0.8073 (t80) REVERT: X 393 GLN cc_start: 0.8730 (mp10) cc_final: 0.7911 (tp-100) REVERT: X 394 TRP cc_start: 0.8038 (m-10) cc_final: 0.7698 (m-10) REVERT: X 404 LEU cc_start: 0.7946 (mp) cc_final: 0.7583 (pp) REVERT: X 413 THR cc_start: 0.8957 (m) cc_final: 0.8744 (t) REVERT: X 491 ARG cc_start: 0.7367 (mtt180) cc_final: 0.7148 (mtt-85) REVERT: X 527 MET cc_start: 0.8574 (mtm) cc_final: 0.7308 (mtm) REVERT: X 544 MET cc_start: 0.7832 (mmp) cc_final: 0.7557 (mmp) REVERT: X 549 MET cc_start: 0.9166 (mpp) cc_final: 0.8833 (mmt) REVERT: X 552 PHE cc_start: 0.8982 (t80) cc_final: 0.8057 (t80) REVERT: X 554 LYS cc_start: 0.9324 (tmtt) cc_final: 0.9025 (tptp) REVERT: X 617 ARG cc_start: 0.8516 (mmt-90) cc_final: 0.8231 (mmt-90) REVERT: X 623 GLU cc_start: 0.8444 (mp0) cc_final: 0.7692 (mm-30) REVERT: X 662 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8460 (pt0) REVERT: X 673 TYR cc_start: 0.8551 (m-80) cc_final: 0.8171 (m-80) REVERT: X 698 PHE cc_start: 0.8925 (p90) cc_final: 0.8693 (p90) REVERT: X 722 ILE cc_start: 0.8165 (mm) cc_final: 0.7508 (tp) REVERT: X 727 LEU cc_start: 0.8963 (mm) cc_final: 0.8636 (mm) REVERT: X 748 ASP cc_start: 0.8868 (t0) cc_final: 0.8439 (t0) REVERT: X 772 MET cc_start: 0.8644 (mtm) cc_final: 0.8133 (mtm) REVERT: Y 1 MET cc_start: 0.7499 (tpt) cc_final: 0.6958 (tpt) REVERT: Y 5 ILE cc_start: 0.7989 (mm) cc_final: 0.7767 (mm) REVERT: Y 64 LEU cc_start: 0.9153 (pp) cc_final: 0.8822 (pp) REVERT: Y 94 GLU cc_start: 0.8309 (tt0) cc_final: 0.7119 (tm-30) REVERT: Y 101 ARG cc_start: 0.8558 (mpt180) cc_final: 0.7873 (mpt180) REVERT: Y 116 ASN cc_start: 0.8115 (m-40) cc_final: 0.7673 (t0) REVERT: Y 128 LEU cc_start: 0.7730 (tt) cc_final: 0.7100 (pp) REVERT: Y 142 ASP cc_start: 0.7261 (t0) cc_final: 0.6643 (t0) REVERT: Y 170 HIS cc_start: 0.7887 (t70) cc_final: 0.7279 (t70) REVERT: Y 208 ILE cc_start: 0.8885 (mm) cc_final: 0.8630 (mm) REVERT: Y 215 LYS cc_start: 0.9045 (tttt) cc_final: 0.8792 (tttt) REVERT: Y 246 TYR cc_start: 0.6824 (t80) cc_final: 0.6299 (t80) REVERT: Y 263 LYS cc_start: 0.7660 (tptt) cc_final: 0.7356 (tppt) REVERT: Y 266 GLN cc_start: 0.6514 (tm-30) cc_final: 0.6310 (tm-30) REVERT: Y 269 ARG cc_start: 0.7096 (tpt90) cc_final: 0.6636 (tpp-160) REVERT: Y 275 PHE cc_start: 0.7305 (t80) cc_final: 0.6980 (t80) REVERT: Y 277 PHE cc_start: 0.7507 (t80) cc_final: 0.7077 (t80) REVERT: Y 297 LYS cc_start: 0.8295 (mmpt) cc_final: 0.7734 (mmtm) REVERT: Y 338 VAL cc_start: 0.8383 (p) cc_final: 0.8099 (m) REVERT: Y 346 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8267 (ptpp) REVERT: Y 433 GLU cc_start: 0.7575 (pt0) cc_final: 0.7261 (pt0) REVERT: Y 434 GLU cc_start: 0.8157 (pm20) cc_final: 0.7894 (mm-30) REVERT: Y 444 LEU cc_start: 0.9165 (tp) cc_final: 0.8558 (pp) REVERT: Y 505 PHE cc_start: 0.8869 (m-10) cc_final: 0.8514 (m-10) REVERT: Y 552 PHE cc_start: 0.7361 (t80) cc_final: 0.6839 (t80) REVERT: Y 591 TRP cc_start: 0.8560 (m-90) cc_final: 0.7512 (m-90) REVERT: Y 617 ARG cc_start: 0.8684 (tpm170) cc_final: 0.8389 (tpm170) REVERT: Y 618 ARG cc_start: 0.9567 (mtp180) cc_final: 0.9349 (mtp180) REVERT: Y 649 THR cc_start: 0.7986 (t) cc_final: 0.7647 (p) REVERT: Y 662 GLU cc_start: 0.8940 (pm20) cc_final: 0.8733 (pm20) REVERT: Y 718 ILE cc_start: 0.8470 (mm) cc_final: 0.8179 (mm) REVERT: Y 729 ASN cc_start: 0.8534 (m-40) cc_final: 0.8262 (t0) REVERT: Y 762 ILE cc_start: 0.8106 (pt) cc_final: 0.7660 (pt) REVERT: Y 774 CYS cc_start: 0.6496 (p) cc_final: 0.6263 (p) REVERT: Z 11 THR cc_start: 0.8417 (m) cc_final: 0.7305 (m) REVERT: Z 14 TYR cc_start: 0.8051 (p90) cc_final: 0.7107 (p90) REVERT: Z 189 TYR cc_start: 0.9438 (m-10) cc_final: 0.9160 (m-10) REVERT: Z 219 TYR cc_start: 0.7506 (m-10) cc_final: 0.7045 (m-80) REVERT: Z 267 TYR cc_start: 0.7792 (m-80) cc_final: 0.7569 (m-80) REVERT: Z 276 LYS cc_start: 0.7827 (ptmm) cc_final: 0.6481 (ptmm) REVERT: Z 301 TYR cc_start: 0.7732 (m-10) cc_final: 0.7529 (m-10) REVERT: Z 356 TRP cc_start: 0.6738 (m100) cc_final: 0.5602 (m100) REVERT: Z 380 CYS cc_start: 0.7830 (t) cc_final: 0.7164 (p) REVERT: Z 500 GLU cc_start: 0.8935 (pp20) cc_final: 0.8556 (pp20) REVERT: Z 501 LEU cc_start: 0.8717 (mt) cc_final: 0.8456 (mt) REVERT: Z 530 MET cc_start: 0.9009 (tpt) cc_final: 0.8670 (tpp) REVERT: Z 549 MET cc_start: 0.8755 (ppp) cc_final: 0.8277 (ppp) REVERT: Z 591 TRP cc_start: 0.7490 (m-10) cc_final: 0.7103 (m-10) REVERT: Z 617 ARG cc_start: 0.8067 (ptm160) cc_final: 0.7777 (ptm160) REVERT: Z 622 LYS cc_start: 0.8814 (mmpt) cc_final: 0.8403 (mmpt) REVERT: Z 623 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8121 (mm-30) REVERT: Z 624 MET cc_start: 0.8129 (ptp) cc_final: 0.7738 (ptp) REVERT: Z 627 GLN cc_start: 0.8064 (pp30) cc_final: 0.7359 (pp30) REVERT: Z 629 GLU cc_start: 0.7780 (mp0) cc_final: 0.7296 (mp0) REVERT: Z 673 TYR cc_start: 0.7690 (m-10) cc_final: 0.7367 (m-10) REVERT: Z 721 ILE cc_start: 0.7910 (mp) cc_final: 0.7148 (mp) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 0.1305 time to fit residues: 78.3880 Evaluate side-chains 370 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 170 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 8 optimal weight: 0.0370 chunk 72 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 97 ASN X 180 GLN ** X 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 315 HIS ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 422 ASN ** X 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN ** Y 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 436 HIS ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 729 ASN ** Y 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 436 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 757 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.139033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.105343 restraints weight = 55457.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.109878 restraints weight = 40431.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113470 restraints weight = 31216.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.116333 restraints weight = 25074.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.118553 restraints weight = 20722.865| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.143 18117 Z= 0.253 Angle : 0.860 10.747 24626 Z= 0.448 Chirality : 0.052 0.217 2820 Planarity : 0.006 0.083 3186 Dihedral : 6.616 29.769 2447 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 31.66 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.46 % Favored : 86.32 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.69 (0.16), residues: 2244 helix: -1.00 (0.20), residues: 567 sheet: -2.62 (0.22), residues: 474 loop : -3.19 (0.16), residues: 1203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG Z 443 TYR 0.020 0.002 TYR Y 734 PHE 0.030 0.002 PHE Z 277 TRP 0.031 0.003 TRP Y 262 HIS 0.018 0.004 HIS X 315 Details of bonding type rmsd covalent geometry : bond 0.00524 (18116) covalent geometry : angle 0.86034 (24626) hydrogen bonds : bond 0.04845 ( 550) hydrogen bonds : angle 6.79941 ( 1524) Misc. bond : bond 0.00121 ( 1) *********************** 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 414 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 10 LEU cc_start: 0.8863 (tt) cc_final: 0.8545 (mm) REVERT: X 18 LEU cc_start: 0.8494 (mt) cc_final: 0.8267 (mt) REVERT: X 40 PHE cc_start: 0.7962 (p90) cc_final: 0.7462 (p90) REVERT: X 194 TYR cc_start: 0.7448 (m-10) cc_final: 0.7131 (m-10) REVERT: X 199 MET cc_start: 0.7858 (ppp) cc_final: 0.7572 (ppp) REVERT: X 215 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8200 (mtmm) REVERT: X 219 TYR cc_start: 0.8658 (m-80) cc_final: 0.8374 (m-80) REVERT: X 222 ASN cc_start: 0.8900 (m-40) cc_final: 0.8466 (p0) REVERT: X 228 GLN cc_start: 0.8033 (pm20) cc_final: 0.7809 (pm20) REVERT: X 291 TRP cc_start: 0.7890 (m-10) cc_final: 0.7487 (m-10) REVERT: X 303 TYR cc_start: 0.7111 (m-10) cc_final: 0.6848 (m-80) REVERT: X 305 TYR cc_start: 0.8049 (m-10) cc_final: 0.7307 (m-10) REVERT: X 347 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8357 (mm-30) REVERT: X 358 ASP cc_start: 0.7573 (m-30) cc_final: 0.6967 (m-30) REVERT: X 375 LEU cc_start: 0.8116 (mm) cc_final: 0.7850 (mm) REVERT: X 376 ASN cc_start: 0.7996 (t0) cc_final: 0.7499 (t0) REVERT: X 385 TYR cc_start: 0.8384 (t80) cc_final: 0.8080 (t80) REVERT: X 394 TRP cc_start: 0.8176 (m-10) cc_final: 0.7965 (m-10) REVERT: X 429 ARG cc_start: 0.9082 (ppt170) cc_final: 0.8877 (ttp80) REVERT: X 491 ARG cc_start: 0.7215 (mtt180) cc_final: 0.6776 (mtt-85) REVERT: X 527 MET cc_start: 0.8694 (mtm) cc_final: 0.7479 (mtm) REVERT: X 539 ASP cc_start: 0.9394 (t70) cc_final: 0.9179 (t0) REVERT: X 544 MET cc_start: 0.7821 (mmp) cc_final: 0.7551 (mmp) REVERT: X 549 MET cc_start: 0.9318 (mpp) cc_final: 0.8894 (mmp) REVERT: X 554 LYS cc_start: 0.9345 (tmtt) cc_final: 0.9076 (tptp) REVERT: X 622 LYS cc_start: 0.9028 (ptpp) cc_final: 0.8752 (ptpt) REVERT: X 623 GLU cc_start: 0.8614 (mp0) cc_final: 0.7627 (mm-30) REVERT: X 662 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8493 (pt0) REVERT: X 666 LYS cc_start: 0.8810 (pptt) cc_final: 0.8591 (ptmm) REVERT: X 667 PHE cc_start: 0.8844 (m-10) cc_final: 0.8397 (m-10) REVERT: X 673 TYR cc_start: 0.8507 (m-80) cc_final: 0.8199 (m-80) REVERT: X 706 GLN cc_start: 0.8317 (mm-40) cc_final: 0.8064 (mm-40) REVERT: X 738 LYS cc_start: 0.8437 (mmpt) cc_final: 0.8235 (mmmt) REVERT: X 748 ASP cc_start: 0.8925 (t0) cc_final: 0.8406 (t0) REVERT: X 772 MET cc_start: 0.8714 (mtm) cc_final: 0.8293 (mtm) REVERT: Y 5 ILE cc_start: 0.8320 (mm) cc_final: 0.7980 (mm) REVERT: Y 94 GLU cc_start: 0.8436 (tt0) cc_final: 0.7160 (tm-30) REVERT: Y 101 ARG cc_start: 0.8787 (mpt180) cc_final: 0.7796 (mpt180) REVERT: Y 107 LEU cc_start: 0.8406 (tp) cc_final: 0.8104 (mm) REVERT: Y 116 ASN cc_start: 0.8202 (m-40) cc_final: 0.7672 (t0) REVERT: Y 128 LEU cc_start: 0.7842 (tt) cc_final: 0.7140 (pp) REVERT: Y 142 ASP cc_start: 0.7430 (t0) cc_final: 0.6861 (t0) REVERT: Y 151 SER cc_start: 0.7770 (p) cc_final: 0.7540 (p) REVERT: Y 159 LEU cc_start: 0.9219 (mp) cc_final: 0.8849 (tp) REVERT: Y 208 ILE cc_start: 0.8793 (mm) cc_final: 0.8560 (mm) REVERT: Y 213 GLU cc_start: 0.7496 (mt-10) cc_final: 0.6386 (mm-30) REVERT: Y 275 PHE cc_start: 0.7349 (t80) cc_final: 0.6713 (t80) REVERT: Y 277 PHE cc_start: 0.7396 (t80) cc_final: 0.6941 (t80) REVERT: Y 338 VAL cc_start: 0.8317 (p) cc_final: 0.7995 (m) REVERT: Y 344 VAL cc_start: 0.7948 (t) cc_final: 0.7705 (t) REVERT: Y 348 ASN cc_start: 0.8791 (p0) cc_final: 0.8540 (p0) REVERT: Y 444 LEU cc_start: 0.9097 (tp) cc_final: 0.8548 (pp) REVERT: Y 454 ASP cc_start: 0.4553 (p0) cc_final: 0.4353 (p0) REVERT: Y 462 TYR cc_start: 0.6237 (m-10) cc_final: 0.5583 (m-80) REVERT: Y 503 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8024 (mt-10) REVERT: Y 505 PHE cc_start: 0.8825 (m-10) cc_final: 0.8323 (m-10) REVERT: Y 527 MET cc_start: 0.9029 (mmp) cc_final: 0.8609 (mmp) REVERT: Y 552 PHE cc_start: 0.7444 (t80) cc_final: 0.6923 (t80) REVERT: Y 617 ARG cc_start: 0.8820 (tpm170) cc_final: 0.8482 (tpm170) REVERT: Y 618 ARG cc_start: 0.9544 (mtp180) cc_final: 0.9270 (ttm-80) REVERT: Y 649 THR cc_start: 0.7990 (t) cc_final: 0.7723 (p) REVERT: Y 662 GLU cc_start: 0.8948 (pm20) cc_final: 0.8708 (pm20) REVERT: Z 1 MET cc_start: 0.8533 (tmm) cc_final: 0.8319 (tmm) REVERT: Z 11 THR cc_start: 0.8610 (m) cc_final: 0.7831 (m) REVERT: Z 14 TYR cc_start: 0.8310 (p90) cc_final: 0.7513 (p90) REVERT: Z 27 SER cc_start: 0.6283 (t) cc_final: 0.5939 (p) REVERT: Z 82 MET cc_start: 0.6321 (mpp) cc_final: 0.5620 (mpp) REVERT: Z 189 TYR cc_start: 0.9371 (m-10) cc_final: 0.9053 (m-10) REVERT: Z 199 MET cc_start: 0.8626 (mmp) cc_final: 0.7951 (tmm) REVERT: Z 219 TYR cc_start: 0.7679 (m-10) cc_final: 0.7053 (m-80) REVERT: Z 267 TYR cc_start: 0.8185 (m-80) cc_final: 0.7449 (m-80) REVERT: Z 276 LYS cc_start: 0.8114 (ptmm) cc_final: 0.6941 (pttt) REVERT: Z 296 PHE cc_start: 0.8399 (m-80) cc_final: 0.8024 (m-10) REVERT: Z 342 PHE cc_start: 0.7689 (t80) cc_final: 0.7343 (t80) REVERT: Z 356 TRP cc_start: 0.6628 (m100) cc_final: 0.5580 (m100) REVERT: Z 380 CYS cc_start: 0.8200 (t) cc_final: 0.7917 (p) REVERT: Z 422 ASN cc_start: 0.8712 (p0) cc_final: 0.8458 (p0) REVERT: Z 430 LEU cc_start: 0.8754 (mt) cc_final: 0.8548 (mm) REVERT: Z 446 ARG cc_start: 0.8125 (mpt180) cc_final: 0.7869 (mpt180) REVERT: Z 477 ASN cc_start: 0.8417 (t0) cc_final: 0.8038 (t0) REVERT: Z 479 ASP cc_start: 0.8986 (m-30) cc_final: 0.8397 (m-30) REVERT: Z 512 ILE cc_start: 0.8144 (mt) cc_final: 0.7766 (mm) REVERT: Z 530 MET cc_start: 0.8964 (tpt) cc_final: 0.8588 (tpp) REVERT: Z 550 LYS cc_start: 0.8687 (tmtt) cc_final: 0.8475 (mmtm) REVERT: Z 551 LYS cc_start: 0.7799 (ptpp) cc_final: 0.7554 (ptpp) REVERT: Z 591 TRP cc_start: 0.7706 (m-10) cc_final: 0.7313 (m-10) REVERT: Z 617 ARG cc_start: 0.8097 (ptm160) cc_final: 0.7550 (ptm160) REVERT: Z 620 ARG cc_start: 0.8700 (mtp180) cc_final: 0.8299 (mtt180) REVERT: Z 622 LYS cc_start: 0.8886 (mmpt) cc_final: 0.8477 (mmpt) REVERT: Z 623 GLU cc_start: 0.8923 (mm-30) cc_final: 0.8191 (mm-30) REVERT: Z 624 MET cc_start: 0.8288 (ptp) cc_final: 0.7955 (ptp) REVERT: Z 627 GLN cc_start: 0.7927 (pp30) cc_final: 0.7216 (pp30) REVERT: Z 629 GLU cc_start: 0.7911 (mp0) cc_final: 0.7405 (mp0) REVERT: Z 647 LYS cc_start: 0.8414 (tptm) cc_final: 0.8019 (pttt) REVERT: Z 673 TYR cc_start: 0.7866 (m-10) cc_final: 0.7503 (m-10) REVERT: Z 721 ILE cc_start: 0.7986 (mp) cc_final: 0.7394 (mp) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.1395 time to fit residues: 83.9731 Evaluate side-chains 372 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 26 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 209 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 207 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 174 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 414 GLN ** 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 436 HIS Y 506 ASN ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 773 GLN Z 315 HIS Z 757 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.142421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.109071 restraints weight = 55732.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.113686 restraints weight = 40547.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.117311 restraints weight = 31256.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.120091 restraints weight = 25035.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.122362 restraints weight = 20656.873| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.4797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 18117 Z= 0.173 Angle : 0.819 11.218 24626 Z= 0.419 Chirality : 0.051 0.210 2820 Planarity : 0.006 0.080 3186 Dihedral : 6.386 30.283 2447 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 25.12 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.94 % Favored : 87.79 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.65 (0.16), residues: 2244 helix: -0.97 (0.20), residues: 569 sheet: -2.57 (0.21), residues: 482 loop : -3.19 (0.16), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG X 775 TYR 0.024 0.002 TYR Y 734 PHE 0.061 0.002 PHE Y 667 TRP 0.042 0.003 TRP Y 262 HIS 0.012 0.002 HIS Y 170 Details of bonding type rmsd covalent geometry : bond 0.00376 (18116) covalent geometry : angle 0.81913 (24626) hydrogen bonds : bond 0.04099 ( 550) hydrogen bonds : angle 6.47352 ( 1524) Misc. bond : bond 0.00096 ( 1) ********************** 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 : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: X 10 LEU cc_start: 0.8862 (tt) cc_final: 0.8552 (mm) REVERT: X 18 LEU cc_start: 0.8493 (mt) cc_final: 0.8264 (mt) REVERT: X 40 PHE cc_start: 0.7879 (p90) cc_final: 0.6939 (p90) REVERT: X 42 GLN cc_start: 0.9223 (pm20) cc_final: 0.8848 (pm20) REVERT: X 74 PHE cc_start: 0.9085 (t80) cc_final: 0.8784 (t80) REVERT: X 75 ASN cc_start: 0.8304 (p0) cc_final: 0.7662 (p0) REVERT: X 194 TYR cc_start: 0.7369 (m-10) cc_final: 0.7124 (m-10) REVERT: X 199 MET cc_start: 0.7708 (ppp) cc_final: 0.7468 (ppp) REVERT: X 215 LYS cc_start: 0.8439 (mtmm) cc_final: 0.8182 (mtmm) REVERT: X 219 TYR cc_start: 0.8519 (m-80) cc_final: 0.8197 (m-80) REVERT: X 222 ASN cc_start: 0.8827 (m-40) cc_final: 0.8383 (p0) REVERT: X 277 PHE cc_start: 0.8498 (m-80) cc_final: 0.8015 (m-80) REVERT: X 291 TRP cc_start: 0.7701 (m-10) cc_final: 0.7381 (m-10) REVERT: X 303 TYR cc_start: 0.6754 (m-10) cc_final: 0.6512 (m-80) REVERT: X 305 TYR cc_start: 0.7820 (m-10) cc_final: 0.7124 (m-10) REVERT: X 347 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8337 (mm-30) REVERT: X 356 TRP cc_start: 0.7449 (m100) cc_final: 0.7206 (m100) REVERT: X 375 LEU cc_start: 0.7956 (mm) cc_final: 0.7676 (mm) REVERT: X 376 ASN cc_start: 0.8180 (t0) cc_final: 0.7834 (t0) REVERT: X 385 TYR cc_start: 0.8304 (t80) cc_final: 0.8023 (t80) REVERT: X 393 GLN cc_start: 0.8892 (mp10) cc_final: 0.8035 (tp-100) REVERT: X 394 TRP cc_start: 0.8183 (m-10) cc_final: 0.7776 (m-10) REVERT: X 404 LEU cc_start: 0.8056 (mp) cc_final: 0.7541 (mm) REVERT: X 491 ARG cc_start: 0.7171 (mtt180) cc_final: 0.6738 (mtt-85) REVERT: X 527 MET cc_start: 0.8573 (mtm) cc_final: 0.7203 (mtm) REVERT: X 544 MET cc_start: 0.7770 (mmp) cc_final: 0.7478 (mmp) REVERT: X 549 MET cc_start: 0.9188 (mpp) cc_final: 0.8847 (mmt) REVERT: X 554 LYS cc_start: 0.9313 (tmtt) cc_final: 0.9016 (tptp) REVERT: X 617 ARG cc_start: 0.8556 (mmt-90) cc_final: 0.8086 (mmt-90) REVERT: X 623 GLU cc_start: 0.8462 (mp0) cc_final: 0.7570 (mm-30) REVERT: X 662 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8452 (pt0) REVERT: X 666 LYS cc_start: 0.8765 (pptt) cc_final: 0.8495 (ptmm) REVERT: X 673 TYR cc_start: 0.8481 (m-80) cc_final: 0.8104 (m-80) REVERT: X 698 PHE cc_start: 0.8819 (p90) cc_final: 0.8614 (p90) REVERT: X 706 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7927 (mm-40) REVERT: X 710 ASP cc_start: 0.8453 (m-30) cc_final: 0.8191 (m-30) REVERT: X 722 ILE cc_start: 0.8177 (mp) cc_final: 0.7696 (tp) REVERT: X 738 LYS cc_start: 0.8453 (mmpt) cc_final: 0.8188 (mmmt) REVERT: X 748 ASP cc_start: 0.8831 (t0) cc_final: 0.8320 (t0) REVERT: X 770 LEU cc_start: 0.9479 (mt) cc_final: 0.9044 (mt) REVERT: X 772 MET cc_start: 0.8665 (mtm) cc_final: 0.8140 (mtm) REVERT: X 773 GLN cc_start: 0.8658 (pm20) cc_final: 0.8194 (pm20) REVERT: Y 1 MET cc_start: 0.7396 (tpt) cc_final: 0.6819 (tpt) REVERT: Y 5 ILE cc_start: 0.7866 (mm) cc_final: 0.7556 (mm) REVERT: Y 94 GLU cc_start: 0.8373 (tt0) cc_final: 0.7056 (tm-30) REVERT: Y 101 ARG cc_start: 0.8742 (mpt180) cc_final: 0.7673 (mpt180) REVERT: Y 107 LEU cc_start: 0.8260 (tp) cc_final: 0.7963 (mm) REVERT: Y 116 ASN cc_start: 0.8243 (m-40) cc_final: 0.7786 (t0) REVERT: Y 128 LEU cc_start: 0.7816 (tt) cc_final: 0.7142 (pp) REVERT: Y 142 ASP cc_start: 0.7305 (t0) cc_final: 0.6749 (t0) REVERT: Y 151 SER cc_start: 0.7698 (p) cc_final: 0.7477 (p) REVERT: Y 159 LEU cc_start: 0.9243 (mp) cc_final: 0.8855 (tp) REVERT: Y 170 HIS cc_start: 0.8244 (t70) cc_final: 0.7754 (t70) REVERT: Y 208 ILE cc_start: 0.8695 (mm) cc_final: 0.8443 (mm) REVERT: Y 269 ARG cc_start: 0.7369 (tpt90) cc_final: 0.7065 (tpp-160) REVERT: Y 275 PHE cc_start: 0.7220 (t80) cc_final: 0.6494 (t80) REVERT: Y 277 PHE cc_start: 0.7373 (t80) cc_final: 0.6905 (t80) REVERT: Y 338 VAL cc_start: 0.8282 (p) cc_final: 0.7981 (m) REVERT: Y 344 VAL cc_start: 0.7729 (t) cc_final: 0.7485 (t) REVERT: Y 444 LEU cc_start: 0.9105 (tp) cc_final: 0.8573 (pp) REVERT: Y 462 TYR cc_start: 0.5875 (m-10) cc_final: 0.5132 (m-80) REVERT: Y 503 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7940 (mt-10) REVERT: Y 505 PHE cc_start: 0.8819 (m-10) cc_final: 0.8393 (m-80) REVERT: Y 506 ASN cc_start: 0.8798 (m-40) cc_final: 0.8597 (m110) REVERT: Y 527 MET cc_start: 0.8902 (mmp) cc_final: 0.8372 (mmp) REVERT: Y 552 PHE cc_start: 0.7239 (t80) cc_final: 0.6899 (t80) REVERT: Y 617 ARG cc_start: 0.8775 (tpm170) cc_final: 0.8455 (tpm170) REVERT: Y 618 ARG cc_start: 0.9537 (mtp180) cc_final: 0.9250 (ttm170) REVERT: Y 631 MET cc_start: 0.8792 (mpp) cc_final: 0.8399 (mpp) REVERT: Y 649 THR cc_start: 0.7969 (t) cc_final: 0.7695 (p) REVERT: Y 729 ASN cc_start: 0.8507 (m110) cc_final: 0.8183 (t0) REVERT: Y 762 ILE cc_start: 0.8192 (pt) cc_final: 0.7596 (pt) REVERT: Z 11 THR cc_start: 0.8595 (m) cc_final: 0.7604 (m) REVERT: Z 14 TYR cc_start: 0.8305 (p90) cc_final: 0.7335 (p90) REVERT: Z 27 SER cc_start: 0.6217 (t) cc_final: 0.5890 (p) REVERT: Z 82 MET cc_start: 0.5739 (mpp) cc_final: 0.4926 (mpp) REVERT: Z 189 TYR cc_start: 0.9404 (m-10) cc_final: 0.9031 (m-10) REVERT: Z 199 MET cc_start: 0.8628 (mmp) cc_final: 0.8291 (tpt) REVERT: Z 219 TYR cc_start: 0.7628 (m-10) cc_final: 0.7053 (m-80) REVERT: Z 265 MET cc_start: 0.7578 (mpp) cc_final: 0.5739 (mpp) REVERT: Z 267 TYR cc_start: 0.8219 (m-80) cc_final: 0.7436 (m-80) REVERT: Z 276 LYS cc_start: 0.7987 (ptmm) cc_final: 0.7098 (ptmt) REVERT: Z 296 PHE cc_start: 0.8354 (m-80) cc_final: 0.8088 (m-10) REVERT: Z 301 TYR cc_start: 0.7733 (m-10) cc_final: 0.7508 (m-10) REVERT: Z 379 MET cc_start: 0.8197 (pmm) cc_final: 0.7700 (pmm) REVERT: Z 380 CYS cc_start: 0.8547 (t) cc_final: 0.7936 (p) REVERT: Z 421 LEU cc_start: 0.8574 (mt) cc_final: 0.8329 (mt) REVERT: Z 422 ASN cc_start: 0.8617 (p0) cc_final: 0.8227 (p0) REVERT: Z 479 ASP cc_start: 0.9004 (m-30) cc_final: 0.8636 (m-30) REVERT: Z 512 ILE cc_start: 0.8080 (mt) cc_final: 0.7687 (mm) REVERT: Z 530 MET cc_start: 0.8950 (tpt) cc_final: 0.8574 (tpp) REVERT: Z 550 LYS cc_start: 0.8742 (tmtt) cc_final: 0.8403 (tptp) REVERT: Z 591 TRP cc_start: 0.7716 (m-10) cc_final: 0.7294 (m-10) REVERT: Z 617 ARG cc_start: 0.8075 (ptm160) cc_final: 0.7654 (ptm160) REVERT: Z 620 ARG cc_start: 0.8698 (mtp180) cc_final: 0.8094 (mtt180) REVERT: Z 622 LYS cc_start: 0.8863 (mmpt) cc_final: 0.8467 (mmpt) REVERT: Z 623 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8164 (mm-30) REVERT: Z 624 MET cc_start: 0.8358 (ptp) cc_final: 0.7975 (ptp) REVERT: Z 627 GLN cc_start: 0.7928 (pp30) cc_final: 0.7045 (pp30) REVERT: Z 629 GLU cc_start: 0.7892 (mp0) cc_final: 0.7492 (mp0) REVERT: Z 647 LYS cc_start: 0.8273 (tptm) cc_final: 0.7764 (pttt) REVERT: Z 673 TYR cc_start: 0.7817 (m-10) cc_final: 0.7489 (m-10) REVERT: Z 721 ILE cc_start: 0.8041 (mp) cc_final: 0.7197 (mp) REVERT: Z 722 ILE cc_start: 0.7331 (mm) cc_final: 0.6807 (tp) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.1364 time to fit residues: 79.3068 Evaluate side-chains 363 residues out of total 2007 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 363 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 16 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 182 optimal weight: 0.0000 chunk 54 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 2 optimal weight: 0.8980 chunk 64 optimal weight: 7.9990 chunk 113 optimal weight: 0.0980 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 188 HIS ** X 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 97 ASN ** Y 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 677 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 677 ASN Z 757 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.147778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.114142 restraints weight = 56415.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.118968 restraints weight = 41011.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.122707 restraints weight = 31530.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.125638 restraints weight = 25141.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.127924 restraints weight = 20655.486| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18117 Z= 0.143 Angle : 0.812 11.368 24626 Z= 0.408 Chirality : 0.051 0.243 2820 Planarity : 0.006 0.104 3186 Dihedral : 6.064 35.097 2447 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 19.35 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.05 % Favored : 88.68 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.05 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.44 (0.16), residues: 2244 helix: -0.85 (0.21), residues: 571 sheet: -2.12 (0.23), residues: 482 loop : -3.18 (0.16), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG Y 363 TYR 0.022 0.001 TYR Z 301 PHE 0.024 0.002 PHE Z 140 TRP 0.030 0.002 TRP Y 262 HIS 0.009 0.001 HIS Y 315 Details of bonding type rmsd covalent geometry : bond 0.00316 (18116) covalent geometry : angle 0.81169 (24626) hydrogen bonds : bond 0.03797 ( 550) hydrogen bonds : angle 6.11195 ( 1524) Misc. bond : bond 0.00040 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3311.91 seconds wall clock time: 58 minutes 23.59 seconds (3503.59 seconds total)