Starting phenix.real_space_refine on Sun Jul 21 07:53:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jro_36600/07_2024/8jro_36600_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jro_36600/07_2024/8jro_36600.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jro_36600/07_2024/8jro_36600.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jro_36600/07_2024/8jro_36600.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jro_36600/07_2024/8jro_36600_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jro_36600/07_2024/8jro_36600_neut.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 92 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 78 5.16 5 C 8720 2.51 5 N 2294 2.21 5 O 2576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 96": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "C GLU 292": "OE1" <-> "OE2" Residue "C GLU 395": "OE1" <-> "OE2" Residue "C GLU 398": "OE1" <-> "OE2" Residue "C GLU 429": "OE1" <-> "OE2" Residue "C GLU 447": "OE1" <-> "OE2" Residue "C PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 594": "OE1" <-> "OE2" Residue "C GLU 727": "OE1" <-> "OE2" Residue "C GLU 753": "OE1" <-> "OE2" Residue "C GLU 775": "OE1" <-> "OE2" Residue "C GLU 792": "OE1" <-> "OE2" Residue "C GLU 835": "OE1" <-> "OE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "A GLU 138": "OE1" <-> "OE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A GLU 395": "OE1" <-> "OE2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 594": "OE1" <-> "OE2" Residue "A GLU 727": "OE1" <-> "OE2" Residue "A GLU 753": "OE1" <-> "OE2" Residue "A GLU 775": "OE1" <-> "OE2" Residue "A GLU 792": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13672 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "C" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5643 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1191 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "A" Number of atoms: 5643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 689, 5643 Classifications: {'peptide': 689} Link IDs: {'PTRANS': 28, 'TRANS': 660} Chain breaks: 1 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 241 SG CYS D 37 80.979 76.140 92.664 1.00 49.18 S ATOM 266 SG CYS D 40 81.927 73.375 94.938 1.00 52.17 S ATOM 522 SG CYS D 70 83.216 73.440 91.258 1.00 54.24 S ATOM 545 SG CYS D 73 79.724 72.473 91.996 1.00 68.14 S ATOM 864 SG CYS D 110 81.395 73.463 74.747 1.00 60.52 S ATOM 886 SG CYS D 113 83.538 74.743 77.528 1.00 55.65 S ATOM 1148 SG CYS D 143 85.036 73.863 74.071 1.00 71.13 S ATOM 1168 SG CYS D 146 83.912 71.087 76.387 1.00 63.68 S ATOM 7075 SG CYS B 37 62.535 33.102 92.664 1.00 49.18 S ATOM 7100 SG CYS B 40 61.587 35.867 94.938 1.00 52.17 S ATOM 7356 SG CYS B 70 60.298 35.802 91.258 1.00 54.24 S ATOM 7379 SG CYS B 73 63.790 36.769 91.996 1.00 68.14 S ATOM 7698 SG CYS B 110 62.119 35.779 74.747 1.00 60.52 S ATOM 7720 SG CYS B 113 59.976 34.499 77.528 1.00 55.65 S ATOM 7982 SG CYS B 143 58.478 35.379 74.071 1.00 71.13 S ATOM 8002 SG CYS B 146 59.602 38.155 76.387 1.00 63.68 S Time building chain proxies: 7.51, per 1000 atoms: 0.55 Number of scatterers: 13672 At special positions: 0 Unit cell: (144.585, 110.313, 113.526, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 78 16.00 O 2576 8.00 N 2294 7.00 C 8720 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.83 Conformation dependent library (CDL) restraints added in 2.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 70 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 73 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 143 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 146 " pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 40 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 37 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 73 " pdb=" ZN D 202 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 110 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 143 " pdb="ZN ZN D 202 " - pdb=" SG CYS D 146 " Number of angles added : 24 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3176 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 14 sheets defined 61.1% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'D' and resid 18 through 26 removed outlier: 3.779A pdb=" N THR D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU D 25 " --> pdb=" O GLN D 21 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 55 Processing helix chain 'D' and resid 70 through 85 Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 102 through 106 Processing helix chain 'D' and resid 118 through 128 Processing helix chain 'D' and resid 144 through 148 removed outlier: 3.928A pdb=" N ARG D 148 " --> pdb=" O SER D 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 142 removed outlier: 4.049A pdb=" N ILE C 136 " --> pdb=" O LYS C 132 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 142 " --> pdb=" O GLU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.721A pdb=" N ILE C 150 " --> pdb=" O TYR C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 165 removed outlier: 3.879A pdb=" N GLN C 165 " --> pdb=" O GLU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 247 removed outlier: 3.505A pdb=" N THR C 244 " --> pdb=" O ARG C 240 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG C 245 " --> pdb=" O ARG C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 274 removed outlier: 3.543A pdb=" N THR C 254 " --> pdb=" O GLU C 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA C 255 " --> pdb=" O LYS C 251 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL C 261 " --> pdb=" O LEU C 257 " (cutoff:3.500A) Proline residue: C 265 - end of helix removed outlier: 3.563A pdb=" N TYR C 273 " --> pdb=" O CYS C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 removed outlier: 3.545A pdb=" N TYR C 283 " --> pdb=" O ASP C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 284 through 292 removed outlier: 3.561A pdb=" N ILE C 288 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 289 " --> pdb=" O ASN C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 302 removed outlier: 3.759A pdb=" N LEU C 296 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS C 297 " --> pdb=" O ARG C 294 " (cutoff:3.500A) Proline residue: C 299 - end of helix removed outlier: 3.604A pdb=" N LEU C 302 " --> pdb=" O PRO C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 314 removed outlier: 3.669A pdb=" N LEU C 308 " --> pdb=" O MET C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 329 Processing helix chain 'C' and resid 332 through 354 removed outlier: 3.748A pdb=" N PHE C 343 " --> pdb=" O MET C 339 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU C 346 " --> pdb=" O THR C 342 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN C 354 " --> pdb=" O LYS C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 386 removed outlier: 3.724A pdb=" N MET C 377 " --> pdb=" O LYS C 373 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL C 378 " --> pdb=" O CYS C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 414 Processing helix chain 'C' and resid 426 through 433 removed outlier: 3.578A pdb=" N THR C 430 " --> pdb=" O ASP C 426 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU C 431 " --> pdb=" O PRO C 427 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 450 removed outlier: 3.626A pdb=" N ILE C 450 " --> pdb=" O GLU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 456 Processing helix chain 'C' and resid 459 through 469 removed outlier: 3.744A pdb=" N THR C 465 " --> pdb=" O ASP C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 Proline residue: C 481 - end of helix Processing helix chain 'C' and resid 485 through 514 removed outlier: 3.545A pdb=" N GLU C 504 " --> pdb=" O ARG C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 547 removed outlier: 3.816A pdb=" N MET C 542 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET C 545 " --> pdb=" O GLU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 568 through 583 Processing helix chain 'C' and resid 584 through 588 Processing helix chain 'C' and resid 608 through 626 Processing helix chain 'C' and resid 634 through 642 removed outlier: 3.951A pdb=" N TYR C 638 " --> pdb=" O PRO C 634 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET C 642 " --> pdb=" O TYR C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 647 through 649 No H-bonds generated for 'chain 'C' and resid 647 through 649' Processing helix chain 'C' and resid 650 through 655 removed outlier: 4.141A pdb=" N SER C 654 " --> pdb=" O ASP C 650 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 668 removed outlier: 4.184A pdb=" N LEU C 665 " --> pdb=" O SER C 661 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 666 " --> pdb=" O LEU C 662 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 723 removed outlier: 3.815A pdb=" N VAL C 714 " --> pdb=" O ARG C 710 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP C 719 " --> pdb=" O ASN C 715 " (cutoff:3.500A) Processing helix chain 'C' and resid 726 through 742 removed outlier: 4.087A pdb=" N VAL C 740 " --> pdb=" O GLY C 736 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 741 " --> pdb=" O PHE C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 750 Processing helix chain 'C' and resid 751 through 760 removed outlier: 4.066A pdb=" N GLU C 756 " --> pdb=" O PRO C 752 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU C 757 " --> pdb=" O GLU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 766 through 773 Processing helix chain 'C' and resid 784 through 795 removed outlier: 3.730A pdb=" N GLU C 792 " --> pdb=" O ARG C 788 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE C 793 " --> pdb=" O GLU C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 810 Processing helix chain 'C' and resid 819 through 823 Processing helix chain 'C' and resid 854 through 869 removed outlier: 3.519A pdb=" N TYR C 868 " --> pdb=" O LYS C 864 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA C 869 " --> pdb=" O ALA C 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 26 removed outlier: 3.779A pdb=" N THR B 24 " --> pdb=" O PRO B 20 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU B 25 " --> pdb=" O GLN B 21 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 70 through 85 Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 144 through 148 removed outlier: 3.928A pdb=" N ARG B 148 " --> pdb=" O SER B 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 142 removed outlier: 4.049A pdb=" N ILE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU A 142 " --> pdb=" O GLU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 157 removed outlier: 3.721A pdb=" N ILE A 150 " --> pdb=" O TYR A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.879A pdb=" N GLN A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 removed outlier: 3.505A pdb=" N THR A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 245 " --> pdb=" O ARG A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 274 removed outlier: 3.543A pdb=" N THR A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 3.563A pdb=" N TYR A 273 " --> pdb=" O CYS A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.545A pdb=" N TYR A 283 " --> pdb=" O ASP A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 284 through 292 removed outlier: 3.561A pdb=" N ILE A 288 " --> pdb=" O LEU A 284 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 289 " --> pdb=" O ASN A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 3.759A pdb=" N LEU A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N HIS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) Proline residue: A 299 - end of helix removed outlier: 3.604A pdb=" N LEU A 302 " --> pdb=" O PRO A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 removed outlier: 3.669A pdb=" N LEU A 308 " --> pdb=" O MET A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 332 through 354 removed outlier: 3.748A pdb=" N PHE A 343 " --> pdb=" O MET A 339 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 354 " --> pdb=" O LYS A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 386 removed outlier: 3.724A pdb=" N MET A 377 " --> pdb=" O LYS A 373 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 414 Processing helix chain 'A' and resid 426 through 433 removed outlier: 3.578A pdb=" N THR A 430 " --> pdb=" O ASP A 426 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A 431 " --> pdb=" O PRO A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 450 removed outlier: 3.626A pdb=" N ILE A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 Processing helix chain 'A' and resid 459 through 469 removed outlier: 3.744A pdb=" N THR A 465 " --> pdb=" O ASP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 484 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 485 through 514 removed outlier: 3.545A pdb=" N GLU A 504 " --> pdb=" O ARG A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 547 removed outlier: 3.816A pdb=" N MET A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 545 " --> pdb=" O GLU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 568 through 583 Processing helix chain 'A' and resid 584 through 588 Processing helix chain 'A' and resid 608 through 626 Processing helix chain 'A' and resid 634 through 642 removed outlier: 3.951A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N MET A 642 " --> pdb=" O TYR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 655 removed outlier: 4.141A pdb=" N SER A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 removed outlier: 4.184A pdb=" N LEU A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 666 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 723 removed outlier: 3.815A pdb=" N VAL A 714 " --> pdb=" O ARG A 710 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 719 " --> pdb=" O ASN A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 742 removed outlier: 4.087A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 741 " --> pdb=" O PHE A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 760 removed outlier: 4.066A pdb=" N GLU A 756 " --> pdb=" O PRO A 752 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 773 Processing helix chain 'A' and resid 784 through 795 removed outlier: 3.730A pdb=" N GLU A 792 " --> pdb=" O ARG A 788 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 793 " --> pdb=" O GLU A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 810 Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 854 through 869 removed outlier: 3.519A pdb=" N TYR A 868 " --> pdb=" O LYS A 864 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 869 " --> pdb=" O ALA A 865 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 36 through 37 removed outlier: 6.170A pdb=" N GLU D 36 " --> pdb=" O ALA D 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 86 through 90 removed outlier: 3.544A pdb=" N TYR D 88 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG D 109 " --> pdb=" O GLY D 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 387 through 388 removed outlier: 6.583A pdb=" N GLU C 387 " --> pdb=" O ARG C 440 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 522 through 527 Processing sheet with id=AA5, first strand: chain 'C' and resid 590 through 593 removed outlier: 3.717A pdb=" N LEU C 598 " --> pdb=" O ASP C 593 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 681 through 684 Processing sheet with id=AA7, first strand: chain 'C' and resid 775 through 777 removed outlier: 6.651A pdb=" N GLU C 775 " --> pdb=" O ILE C 827 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LYS C 829 " --> pdb=" O GLU C 775 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP C 777 " --> pdb=" O LYS C 829 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE C 826 " --> pdb=" O LEU C 847 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU C 849 " --> pdb=" O ILE C 826 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ALA C 828 " --> pdb=" O LEU C 849 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.170A pdb=" N GLU B 36 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 90 removed outlier: 3.544A pdb=" N TYR B 88 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG B 109 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.583A pdb=" N GLU A 387 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 522 through 527 Processing sheet with id=AB3, first strand: chain 'A' and resid 590 through 593 removed outlier: 3.717A pdb=" N LEU A 598 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 681 through 684 Processing sheet with id=AB5, first strand: chain 'A' and resid 775 through 777 removed outlier: 6.651A pdb=" N GLU A 775 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N LYS A 829 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ASP A 777 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE A 826 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 849 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ALA A 828 " --> pdb=" O LEU A 849 " (cutoff:3.500A) 624 hydrogen bonds defined for protein. 1740 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: 3.79 Time building geometry restraints manager: 5.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4492 1.34 - 1.46: 3034 1.46 - 1.58: 6302 1.58 - 1.70: 0 1.70 - 1.81: 120 Bond restraints: 13948 Sorted by residual: bond pdb=" CB ASN C 275 " pdb=" CG ASN C 275 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.84e-01 bond pdb=" CB ASN A 275 " pdb=" CG ASN A 275 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 6.84e-01 bond pdb=" CB GLN B 27 " pdb=" CG GLN B 27 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.32e-01 bond pdb=" CB GLN D 27 " pdb=" CG GLN D 27 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.32e-01 bond pdb=" CG GLN B 27 " pdb=" CD GLN B 27 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 4.92e-01 ... (remaining 13943 not shown) Histogram of bond angle deviations from ideal: 100.09 - 106.87: 338 106.87 - 113.65: 7544 113.65 - 120.44: 5580 120.44 - 127.22: 5274 127.22 - 134.01: 96 Bond angle restraints: 18832 Sorted by residual: angle pdb=" N VAL C 740 " pdb=" CA VAL C 740 " pdb=" C VAL C 740 " ideal model delta sigma weight residual 113.53 110.06 3.47 9.80e-01 1.04e+00 1.25e+01 angle pdb=" N VAL A 740 " pdb=" CA VAL A 740 " pdb=" C VAL A 740 " ideal model delta sigma weight residual 113.53 110.06 3.47 9.80e-01 1.04e+00 1.25e+01 angle pdb=" N ILE D 30 " pdb=" CA ILE D 30 " pdb=" C ILE D 30 " ideal model delta sigma weight residual 113.07 108.70 4.37 1.36e+00 5.41e-01 1.03e+01 angle pdb=" N ILE B 30 " pdb=" CA ILE B 30 " pdb=" C ILE B 30 " ideal model delta sigma weight residual 113.07 108.70 4.37 1.36e+00 5.41e-01 1.03e+01 angle pdb=" CB MET C 304 " pdb=" CG MET C 304 " pdb=" SD MET C 304 " ideal model delta sigma weight residual 112.70 120.22 -7.52 3.00e+00 1.11e-01 6.28e+00 ... (remaining 18827 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7314 17.94 - 35.88: 902 35.88 - 53.83: 260 53.83 - 71.77: 36 71.77 - 89.71: 16 Dihedral angle restraints: 8528 sinusoidal: 3612 harmonic: 4916 Sorted by residual: dihedral pdb=" CG ARG C 763 " pdb=" CD ARG C 763 " pdb=" NE ARG C 763 " pdb=" CZ ARG C 763 " ideal model delta sinusoidal sigma weight residual -90.00 -133.98 43.98 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CG ARG A 763 " pdb=" CD ARG A 763 " pdb=" NE ARG A 763 " pdb=" CZ ARG A 763 " ideal model delta sinusoidal sigma weight residual -90.00 -133.98 43.98 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA ASP A 813 " pdb=" CB ASP A 813 " pdb=" CG ASP A 813 " pdb=" OD1 ASP A 813 " ideal model delta sinusoidal sigma weight residual -30.00 -84.76 54.76 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 8525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 978 0.024 - 0.048: 634 0.048 - 0.072: 308 0.072 - 0.096: 80 0.096 - 0.119: 60 Chirality restraints: 2060 Sorted by residual: chirality pdb=" CA ILE A 401 " pdb=" N ILE A 401 " pdb=" C ILE A 401 " pdb=" CB ILE A 401 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA ILE C 401 " pdb=" N ILE C 401 " pdb=" C ILE C 401 " pdb=" CB ILE C 401 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA PRO A 481 " pdb=" N PRO A 481 " pdb=" C PRO A 481 " pdb=" CB PRO A 481 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.42e-01 ... (remaining 2057 not shown) Planarity restraints: 2442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 306 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO C 307 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 307 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 307 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 306 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.63e+00 pdb=" N PRO A 307 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 307 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 307 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 744 " -0.020 5.00e-02 4.00e+02 3.05e-02 1.49e+00 pdb=" N PRO A 745 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " -0.017 5.00e-02 4.00e+02 ... (remaining 2439 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 500 2.72 - 3.26: 13760 3.26 - 3.81: 21308 3.81 - 4.35: 27938 4.35 - 4.90: 46188 Nonbonded interactions: 109694 Sorted by model distance: nonbonded pdb=" OH TYR B 86 " pdb=" OG SER B 89 " model vdw 2.174 2.440 nonbonded pdb=" OH TYR D 86 " pdb=" OG SER D 89 " model vdw 2.174 2.440 nonbonded pdb=" OE2 GLU A 303 " pdb=" OH TYR A 349 " model vdw 2.187 2.440 nonbonded pdb=" OE2 GLU C 303 " pdb=" OH TYR C 349 " model vdw 2.187 2.440 nonbonded pdb=" OG1 THR A 679 " pdb=" O GLY A 700 " model vdw 2.218 2.440 ... (remaining 109689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 39.030 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13948 Z= 0.225 Angle : 0.502 7.518 18832 Z= 0.268 Chirality : 0.039 0.119 2060 Planarity : 0.003 0.032 2442 Dihedral : 16.679 89.709 5352 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.26 % Allowed : 20.37 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1648 helix: -0.64 (0.17), residues: 866 sheet: -0.18 (0.60), residues: 92 loop : -0.21 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 328 HIS 0.002 0.000 HIS D 31 PHE 0.012 0.001 PHE A 475 TYR 0.015 0.001 TYR B 77 ARG 0.003 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 389 time to evaluate : 1.633 Fit side-chains revert: symmetry clash REVERT: D 112 ASN cc_start: 0.8667 (m110) cc_final: 0.8433 (m-40) REVERT: C 122 PHE cc_start: 0.7219 (m-80) cc_final: 0.6969 (m-10) REVERT: C 138 GLU cc_start: 0.6982 (tp30) cc_final: 0.6754 (tp30) REVERT: C 268 GLU cc_start: 0.7706 (tt0) cc_final: 0.7019 (tm-30) REVERT: C 301 TYR cc_start: 0.8471 (m-80) cc_final: 0.8256 (m-80) REVERT: C 457 VAL cc_start: 0.8725 (m) cc_final: 0.8187 (p) REVERT: C 459 GLU cc_start: 0.7327 (mm-30) cc_final: 0.7061 (mm-30) REVERT: C 480 CYS cc_start: 0.7669 (p) cc_final: 0.7333 (p) REVERT: C 552 LYS cc_start: 0.8214 (mttp) cc_final: 0.7889 (mttm) REVERT: C 635 MET cc_start: 0.8226 (tpp) cc_final: 0.7979 (tpp) REVERT: C 642 MET cc_start: 0.8956 (mmm) cc_final: 0.8720 (mmm) REVERT: C 712 GLU cc_start: 0.7496 (tt0) cc_final: 0.7235 (tp30) REVERT: C 719 ASP cc_start: 0.8029 (t70) cc_final: 0.7672 (t0) REVERT: C 728 LYS cc_start: 0.8163 (mtmt) cc_final: 0.7902 (mmmm) REVERT: C 766 ASP cc_start: 0.7696 (t0) cc_final: 0.7460 (t0) REVERT: C 793 ILE cc_start: 0.8451 (mt) cc_final: 0.8218 (mt) REVERT: C 822 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7872 (mmtm) REVERT: A 122 PHE cc_start: 0.7092 (m-80) cc_final: 0.6866 (m-10) REVERT: A 262 TYR cc_start: 0.6539 (t80) cc_final: 0.6250 (t80) REVERT: A 268 GLU cc_start: 0.7556 (tt0) cc_final: 0.6906 (tm-30) REVERT: A 387 GLU cc_start: 0.6863 (mt-10) cc_final: 0.6645 (mt-10) REVERT: A 426 ASP cc_start: 0.7361 (t0) cc_final: 0.7006 (t0) REVERT: A 441 LYS cc_start: 0.8442 (tptp) cc_final: 0.8135 (tptp) REVERT: A 457 VAL cc_start: 0.8680 (m) cc_final: 0.8141 (p) REVERT: A 459 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7057 (mm-30) REVERT: A 480 CYS cc_start: 0.7718 (p) cc_final: 0.7443 (p) REVERT: A 525 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8517 (mt) REVERT: A 534 ASP cc_start: 0.7537 (m-30) cc_final: 0.7327 (m-30) REVERT: A 552 LYS cc_start: 0.8274 (mttp) cc_final: 0.7951 (mmtm) REVERT: A 635 MET cc_start: 0.8177 (tpp) cc_final: 0.7898 (tpp) REVERT: A 653 ASP cc_start: 0.7848 (m-30) cc_final: 0.7338 (p0) REVERT: A 667 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7412 (mt-10) REVERT: A 728 LYS cc_start: 0.8255 (mtmt) cc_final: 0.7942 (mmmm) REVERT: A 766 ASP cc_start: 0.7593 (t0) cc_final: 0.7392 (t0) REVERT: A 793 ILE cc_start: 0.8526 (mt) cc_final: 0.8298 (mt) REVERT: A 825 MET cc_start: 0.8392 (ttt) cc_final: 0.8190 (ttt) outliers start: 4 outliers final: 2 residues processed: 389 average time/residue: 0.3330 time to fit residues: 173.8607 Evaluate side-chains 356 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 353 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 742 ASN Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 742 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 148 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN C 321 GLN C 357 ASN C 410 GLN C 451 ASN C 715 ASN C 795 HIS C 845 ASN B 112 ASN A 321 GLN A 357 ASN A 451 ASN A 681 GLN A 715 ASN A 795 HIS A 845 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13948 Z= 0.230 Angle : 0.519 8.090 18832 Z= 0.269 Chirality : 0.040 0.155 2060 Planarity : 0.004 0.036 2442 Dihedral : 4.242 58.055 1852 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.70 % Allowed : 20.95 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1648 helix: 0.12 (0.17), residues: 888 sheet: -0.69 (0.68), residues: 68 loop : -0.15 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 139 HIS 0.002 0.001 HIS B 31 PHE 0.014 0.001 PHE A 797 TYR 0.016 0.001 TYR A 273 ARG 0.005 0.000 ARG A 803 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 366 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7737 (tp) cc_final: 0.7469 (tp) REVERT: D 28 THR cc_start: 0.7705 (OUTLIER) cc_final: 0.7427 (t) REVERT: D 62 ARG cc_start: 0.7805 (mtt-85) cc_final: 0.7517 (mtt90) REVERT: C 235 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6241 (p0) REVERT: C 268 GLU cc_start: 0.7651 (tt0) cc_final: 0.7013 (tm-30) REVERT: C 270 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7064 (t0) REVERT: C 349 TYR cc_start: 0.8223 (t80) cc_final: 0.7992 (t80) REVERT: C 426 ASP cc_start: 0.7416 (t0) cc_final: 0.7035 (t0) REVERT: C 457 VAL cc_start: 0.8639 (m) cc_final: 0.8201 (p) REVERT: C 525 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8519 (mt) REVERT: C 552 LYS cc_start: 0.8130 (mmtp) cc_final: 0.7815 (mttp) REVERT: C 635 MET cc_start: 0.8131 (tpp) cc_final: 0.7874 (tpp) REVERT: C 712 GLU cc_start: 0.7444 (tt0) cc_final: 0.7110 (tp30) REVERT: C 719 ASP cc_start: 0.8108 (t70) cc_final: 0.7729 (t0) REVERT: C 728 LYS cc_start: 0.7986 (mtmt) cc_final: 0.7730 (mmmm) REVERT: C 793 ILE cc_start: 0.8531 (mt) cc_final: 0.8280 (mt) REVERT: B 19 LEU cc_start: 0.7927 (tp) cc_final: 0.7618 (tp) REVERT: B 28 THR cc_start: 0.7742 (OUTLIER) cc_final: 0.7471 (t) REVERT: A 235 ASP cc_start: 0.7185 (OUTLIER) cc_final: 0.6333 (p0) REVERT: A 268 GLU cc_start: 0.7574 (tt0) cc_final: 0.6930 (tm-30) REVERT: A 270 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.7213 (t0) REVERT: A 276 VAL cc_start: 0.7916 (m) cc_final: 0.7694 (m) REVERT: A 300 GLU cc_start: 0.7612 (pt0) cc_final: 0.7378 (pt0) REVERT: A 349 TYR cc_start: 0.8116 (t80) cc_final: 0.7883 (t80) REVERT: A 426 ASP cc_start: 0.7291 (t0) cc_final: 0.6944 (t0) REVERT: A 429 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6732 (tt0) REVERT: A 457 VAL cc_start: 0.8663 (m) cc_final: 0.8192 (p) REVERT: A 459 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6984 (mm-30) REVERT: A 525 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8475 (mt) REVERT: A 552 LYS cc_start: 0.8232 (mmtp) cc_final: 0.7926 (mttp) REVERT: A 595 SER cc_start: 0.8484 (t) cc_final: 0.8242 (p) REVERT: A 635 MET cc_start: 0.8105 (tpp) cc_final: 0.7804 (tpp) REVERT: A 667 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7456 (mt-10) REVERT: A 715 ASN cc_start: 0.8168 (m-40) cc_final: 0.7907 (m-40) REVERT: A 772 GLU cc_start: 0.7647 (tp30) cc_final: 0.7381 (tp30) REVERT: A 775 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7394 (mm-30) REVERT: A 793 ILE cc_start: 0.8582 (mt) cc_final: 0.8334 (mt) outliers start: 26 outliers final: 11 residues processed: 377 average time/residue: 0.3262 time to fit residues: 165.9811 Evaluate side-chains 365 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 346 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 270 ASP Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 491 LEU Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 525 LEU Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 762 SER Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 525 LEU Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 762 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 123 optimal weight: 0.1980 chunk 101 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 161 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 119 optimal weight: 0.0670 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN D 130 GLN C 321 GLN C 547 ASN B 112 ASN A 321 GLN A 547 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13948 Z= 0.188 Angle : 0.484 7.850 18832 Z= 0.247 Chirality : 0.039 0.130 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.969 57.180 1848 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.57 % Allowed : 23.43 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.21), residues: 1648 helix: 0.49 (0.18), residues: 884 sheet: -0.94 (0.64), residues: 72 loop : -0.07 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 139 HIS 0.002 0.000 HIS A 655 PHE 0.016 0.001 PHE C 475 TYR 0.011 0.001 TYR D 77 ARG 0.005 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 361 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7720 (tp) cc_final: 0.7448 (tp) REVERT: D 62 ARG cc_start: 0.7793 (mtt-85) cc_final: 0.7555 (mtt90) REVERT: C 138 GLU cc_start: 0.7327 (tp30) cc_final: 0.7126 (tp30) REVERT: C 235 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6231 (p0) REVERT: C 268 GLU cc_start: 0.7670 (tt0) cc_final: 0.7078 (tm-30) REVERT: C 349 TYR cc_start: 0.8214 (t80) cc_final: 0.7953 (t80) REVERT: C 426 ASP cc_start: 0.7396 (t0) cc_final: 0.7002 (t0) REVERT: C 457 VAL cc_start: 0.8487 (m) cc_final: 0.8179 (p) REVERT: C 541 GLU cc_start: 0.7533 (mm-30) cc_final: 0.7277 (mp0) REVERT: C 552 LYS cc_start: 0.8145 (OUTLIER) cc_final: 0.7861 (mttp) REVERT: C 635 MET cc_start: 0.8172 (tpp) cc_final: 0.7914 (tpp) REVERT: C 719 ASP cc_start: 0.8042 (t70) cc_final: 0.7694 (t0) REVERT: C 728 LYS cc_start: 0.7921 (mtmt) cc_final: 0.7693 (mmmm) REVERT: C 793 ILE cc_start: 0.8558 (mt) cc_final: 0.8239 (mt) REVERT: B 19 LEU cc_start: 0.7901 (tp) cc_final: 0.7607 (tp) REVERT: A 134 TYR cc_start: 0.7797 (m-10) cc_final: 0.7191 (m-10) REVERT: A 235 ASP cc_start: 0.7150 (OUTLIER) cc_final: 0.6337 (p0) REVERT: A 268 GLU cc_start: 0.7597 (tt0) cc_final: 0.6928 (tm-30) REVERT: A 275 ASN cc_start: 0.8246 (t0) cc_final: 0.8037 (t0) REVERT: A 300 GLU cc_start: 0.7662 (pt0) cc_final: 0.7431 (pt0) REVERT: A 349 TYR cc_start: 0.8139 (t80) cc_final: 0.7936 (t80) REVERT: A 426 ASP cc_start: 0.7287 (t0) cc_final: 0.6948 (t0) REVERT: A 429 GLU cc_start: 0.6985 (mt-10) cc_final: 0.6712 (tt0) REVERT: A 457 VAL cc_start: 0.8549 (m) cc_final: 0.8109 (p) REVERT: A 459 GLU cc_start: 0.7235 (mm-30) cc_final: 0.6983 (mm-30) REVERT: A 552 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7992 (mmtm) REVERT: A 595 SER cc_start: 0.8544 (t) cc_final: 0.8274 (p) REVERT: A 635 MET cc_start: 0.8121 (tpp) cc_final: 0.7823 (tpp) REVERT: A 667 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7478 (mt-10) REVERT: A 668 TYR cc_start: 0.6897 (t80) cc_final: 0.6479 (t80) REVERT: A 699 ASN cc_start: 0.7421 (p0) cc_final: 0.7104 (p0) REVERT: A 719 ASP cc_start: 0.7974 (t70) cc_final: 0.7658 (t0) REVERT: A 793 ILE cc_start: 0.8593 (mt) cc_final: 0.8276 (mt) outliers start: 24 outliers final: 14 residues processed: 373 average time/residue: 0.3531 time to fit residues: 174.9294 Evaluate side-chains 364 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 346 time to evaluate : 1.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 251 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 0.2980 chunk 100 optimal weight: 0.0370 chunk 149 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 78 optimal weight: 0.0980 chunk 141 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN D 130 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13948 Z= 0.142 Angle : 0.450 7.724 18832 Z= 0.229 Chirality : 0.038 0.126 2060 Planarity : 0.003 0.035 2442 Dihedral : 3.563 15.868 1846 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.22 % Allowed : 23.56 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1648 helix: 0.87 (0.18), residues: 878 sheet: -0.99 (0.65), residues: 72 loop : 0.10 (0.25), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 139 HIS 0.001 0.000 HIS C 655 PHE 0.017 0.001 PHE A 475 TYR 0.012 0.001 TYR A 694 ARG 0.005 0.000 ARG A 803 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 353 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7730 (tp) cc_final: 0.7465 (tp) REVERT: D 28 THR cc_start: 0.7868 (OUTLIER) cc_final: 0.7631 (t) REVERT: D 62 ARG cc_start: 0.7762 (mtt-85) cc_final: 0.7535 (mtt90) REVERT: C 141 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7426 (ttp80) REVERT: C 235 ASP cc_start: 0.6926 (OUTLIER) cc_final: 0.6085 (p0) REVERT: C 268 GLU cc_start: 0.7766 (tt0) cc_final: 0.7069 (tm-30) REVERT: C 349 TYR cc_start: 0.8236 (t80) cc_final: 0.8001 (t80) REVERT: C 426 ASP cc_start: 0.7348 (t0) cc_final: 0.6969 (t0) REVERT: C 457 VAL cc_start: 0.8447 (m) cc_final: 0.8140 (p) REVERT: C 526 LYS cc_start: 0.8346 (ttpp) cc_final: 0.8140 (tttm) REVERT: C 541 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7255 (mm-30) REVERT: C 552 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7870 (mmtp) REVERT: C 719 ASP cc_start: 0.8028 (t70) cc_final: 0.7682 (t0) REVERT: C 793 ILE cc_start: 0.8513 (mt) cc_final: 0.8134 (mt) REVERT: B 19 LEU cc_start: 0.7893 (tp) cc_final: 0.7598 (tp) REVERT: B 62 ARG cc_start: 0.7836 (mtt-85) cc_final: 0.7573 (mtt90) REVERT: B 136 ARG cc_start: 0.8080 (ttt90) cc_final: 0.7864 (ttm-80) REVERT: A 134 TYR cc_start: 0.7790 (m-10) cc_final: 0.7162 (m-10) REVERT: A 235 ASP cc_start: 0.7050 (OUTLIER) cc_final: 0.6258 (p0) REVERT: A 268 GLU cc_start: 0.7619 (tt0) cc_final: 0.7006 (tm-30) REVERT: A 275 ASN cc_start: 0.8328 (t0) cc_final: 0.8054 (t0) REVERT: A 300 GLU cc_start: 0.7692 (pt0) cc_final: 0.7440 (pt0) REVERT: A 349 TYR cc_start: 0.8156 (t80) cc_final: 0.7887 (t80) REVERT: A 426 ASP cc_start: 0.7277 (t0) cc_final: 0.6887 (t0) REVERT: A 429 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6717 (tt0) REVERT: A 457 VAL cc_start: 0.8558 (m) cc_final: 0.8105 (p) REVERT: A 459 GLU cc_start: 0.7239 (mm-30) cc_final: 0.6964 (mm-30) REVERT: A 526 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8122 (ttpp) REVERT: A 552 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7878 (mmtp) REVERT: A 595 SER cc_start: 0.8510 (t) cc_final: 0.8194 (p) REVERT: A 635 MET cc_start: 0.8129 (tpp) cc_final: 0.7813 (tpp) REVERT: A 667 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7459 (mt-10) REVERT: A 668 TYR cc_start: 0.6907 (t80) cc_final: 0.6506 (t80) REVERT: A 712 GLU cc_start: 0.7501 (tt0) cc_final: 0.7137 (tt0) REVERT: A 719 ASP cc_start: 0.7955 (t70) cc_final: 0.7631 (t0) REVERT: A 793 ILE cc_start: 0.8514 (mt) cc_final: 0.8160 (mt) outliers start: 34 outliers final: 13 residues processed: 372 average time/residue: 0.3481 time to fit residues: 172.0140 Evaluate side-chains 363 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 345 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 425 VAL Chi-restraints excluded: chain C residue 552 LYS Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 747 LYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 762 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 742 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 118 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN C 321 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 ASN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13948 Z= 0.244 Angle : 0.494 8.468 18832 Z= 0.248 Chirality : 0.040 0.134 2060 Planarity : 0.003 0.035 2442 Dihedral : 3.717 17.303 1846 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.42 % Allowed : 23.17 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.21), residues: 1648 helix: 0.74 (0.18), residues: 888 sheet: -1.00 (0.65), residues: 72 loop : -0.02 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 139 HIS 0.003 0.001 HIS C 655 PHE 0.021 0.001 PHE A 475 TYR 0.016 0.001 TYR A 556 ARG 0.005 0.000 ARG A 803 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 360 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7731 (tp) cc_final: 0.7447 (tp) REVERT: D 28 THR cc_start: 0.7696 (OUTLIER) cc_final: 0.7448 (t) REVERT: D 62 ARG cc_start: 0.7724 (mtt-85) cc_final: 0.7395 (mtt90) REVERT: C 141 ARG cc_start: 0.7865 (ttp80) cc_final: 0.7458 (ttp80) REVERT: C 235 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6450 (p0) REVERT: C 268 GLU cc_start: 0.7732 (tt0) cc_final: 0.7077 (tm-30) REVERT: C 349 TYR cc_start: 0.8246 (t80) cc_final: 0.7967 (t80) REVERT: C 426 ASP cc_start: 0.7384 (t0) cc_final: 0.6996 (t70) REVERT: C 457 VAL cc_start: 0.8463 (m) cc_final: 0.8159 (p) REVERT: C 526 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8135 (tttm) REVERT: C 552 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7828 (mmtp) REVERT: C 677 MET cc_start: 0.6622 (mmm) cc_final: 0.6399 (mmm) REVERT: C 699 ASN cc_start: 0.7277 (p0) cc_final: 0.6716 (p0) REVERT: C 719 ASP cc_start: 0.7984 (t70) cc_final: 0.7648 (t0) REVERT: C 793 ILE cc_start: 0.8515 (mt) cc_final: 0.8142 (mt) REVERT: B 19 LEU cc_start: 0.7908 (tp) cc_final: 0.7588 (tp) REVERT: A 134 TYR cc_start: 0.7822 (m-10) cc_final: 0.7209 (m-10) REVERT: A 235 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6436 (p0) REVERT: A 268 GLU cc_start: 0.7591 (tt0) cc_final: 0.6979 (tm-30) REVERT: A 275 ASN cc_start: 0.8373 (t0) cc_final: 0.8120 (t0) REVERT: A 300 GLU cc_start: 0.7741 (pt0) cc_final: 0.7481 (pt0) REVERT: A 311 LYS cc_start: 0.8300 (mtmm) cc_final: 0.8094 (ttmm) REVERT: A 349 TYR cc_start: 0.8143 (t80) cc_final: 0.7907 (t80) REVERT: A 426 ASP cc_start: 0.7326 (t0) cc_final: 0.7032 (t0) REVERT: A 429 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6697 (tt0) REVERT: A 457 VAL cc_start: 0.8561 (m) cc_final: 0.8079 (p) REVERT: A 459 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6952 (mm-30) REVERT: A 552 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7879 (mttp) REVERT: A 595 SER cc_start: 0.8543 (t) cc_final: 0.8201 (p) REVERT: A 635 MET cc_start: 0.8178 (tpp) cc_final: 0.7855 (tpp) REVERT: A 667 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7477 (mt-10) REVERT: A 699 ASN cc_start: 0.7404 (p0) cc_final: 0.7060 (p0) REVERT: A 712 GLU cc_start: 0.7503 (tt0) cc_final: 0.7119 (tt0) REVERT: A 747 LYS cc_start: 0.8471 (mttm) cc_final: 0.8234 (mmmt) REVERT: A 793 ILE cc_start: 0.8525 (mt) cc_final: 0.8165 (mt) outliers start: 37 outliers final: 26 residues processed: 378 average time/residue: 0.3482 time to fit residues: 175.8022 Evaluate side-chains 381 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 351 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain C residue 762 SER Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 339 MET Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 654 SER Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 0.9980 chunk 39 optimal weight: 0.2980 chunk 158 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 83 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 112 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 547 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13948 Z= 0.170 Angle : 0.461 8.910 18832 Z= 0.232 Chirality : 0.039 0.129 2060 Planarity : 0.003 0.035 2442 Dihedral : 3.604 16.335 1846 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.48 % Allowed : 23.63 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1648 helix: 0.90 (0.18), residues: 890 sheet: -1.01 (0.65), residues: 72 loop : 0.12 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 139 HIS 0.002 0.000 HIS A 655 PHE 0.019 0.001 PHE C 475 TYR 0.015 0.001 TYR A 694 ARG 0.008 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 357 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7731 (tp) cc_final: 0.7469 (tp) REVERT: D 112 ASN cc_start: 0.8672 (m-40) cc_final: 0.8425 (m110) REVERT: C 141 ARG cc_start: 0.7868 (ttp80) cc_final: 0.7452 (ttp80) REVERT: C 235 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6692 (p0) REVERT: C 241 ARG cc_start: 0.7940 (ptp90) cc_final: 0.7445 (mtm110) REVERT: C 268 GLU cc_start: 0.7714 (tt0) cc_final: 0.7065 (tm-30) REVERT: C 349 TYR cc_start: 0.8226 (t80) cc_final: 0.7966 (t80) REVERT: C 426 ASP cc_start: 0.7340 (t0) cc_final: 0.6956 (t70) REVERT: C 457 VAL cc_start: 0.8449 (m) cc_final: 0.8160 (p) REVERT: C 526 LYS cc_start: 0.8363 (ttpp) cc_final: 0.8148 (tttm) REVERT: C 552 LYS cc_start: 0.8120 (mmtp) cc_final: 0.7788 (mmtp) REVERT: C 677 MET cc_start: 0.6625 (mmm) cc_final: 0.6367 (mmm) REVERT: C 699 ASN cc_start: 0.7287 (p0) cc_final: 0.6744 (p0) REVERT: C 719 ASP cc_start: 0.7998 (t70) cc_final: 0.7643 (t0) REVERT: C 772 GLU cc_start: 0.7692 (tp30) cc_final: 0.7474 (tp30) REVERT: C 793 ILE cc_start: 0.8497 (mt) cc_final: 0.8105 (mt) REVERT: B 19 LEU cc_start: 0.7896 (tp) cc_final: 0.7595 (tp) REVERT: B 136 ARG cc_start: 0.8049 (ttt90) cc_final: 0.7798 (ttm-80) REVERT: A 134 TYR cc_start: 0.7822 (m-10) cc_final: 0.7182 (m-10) REVERT: A 235 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6355 (p0) REVERT: A 268 GLU cc_start: 0.7592 (tt0) cc_final: 0.6978 (tm-30) REVERT: A 275 ASN cc_start: 0.8366 (t0) cc_final: 0.8096 (t0) REVERT: A 291 MET cc_start: 0.7421 (mmm) cc_final: 0.7054 (mmm) REVERT: A 300 GLU cc_start: 0.7742 (pt0) cc_final: 0.7486 (pt0) REVERT: A 349 TYR cc_start: 0.8096 (t80) cc_final: 0.7845 (t80) REVERT: A 426 ASP cc_start: 0.7315 (t0) cc_final: 0.6958 (t70) REVERT: A 429 GLU cc_start: 0.7013 (mt-10) cc_final: 0.6688 (tt0) REVERT: A 457 VAL cc_start: 0.8578 (m) cc_final: 0.8097 (p) REVERT: A 459 GLU cc_start: 0.7197 (mm-30) cc_final: 0.6916 (mm-30) REVERT: A 525 LEU cc_start: 0.8631 (mt) cc_final: 0.8391 (mp) REVERT: A 526 LYS cc_start: 0.8361 (ttpp) cc_final: 0.8137 (ttpp) REVERT: A 552 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7847 (mttp) REVERT: A 635 MET cc_start: 0.8185 (tpp) cc_final: 0.7881 (tpp) REVERT: A 667 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7435 (mt-10) REVERT: A 699 ASN cc_start: 0.7392 (p0) cc_final: 0.7047 (p0) REVERT: A 712 GLU cc_start: 0.7511 (tt0) cc_final: 0.7148 (tt0) REVERT: A 747 LYS cc_start: 0.8475 (mttm) cc_final: 0.8243 (mmmt) REVERT: A 793 ILE cc_start: 0.8503 (mt) cc_final: 0.8139 (mt) outliers start: 38 outliers final: 27 residues processed: 379 average time/residue: 0.3406 time to fit residues: 173.2275 Evaluate side-chains 381 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 351 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 235 ASP Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 747 LYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 825 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 152 optimal weight: 0.0770 chunk 17 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 158 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 96 optimal weight: 0.0020 chunk 72 optimal weight: 2.9990 overall best weight: 0.5146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 GLN A 321 GLN ** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13948 Z= 0.168 Angle : 0.469 9.882 18832 Z= 0.236 Chirality : 0.039 0.127 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.582 15.994 1846 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.61 % Allowed : 23.37 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1648 helix: 1.02 (0.18), residues: 892 sheet: -1.01 (0.65), residues: 72 loop : 0.14 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 600 HIS 0.002 0.000 HIS C 655 PHE 0.021 0.001 PHE C 475 TYR 0.015 0.001 TYR C 852 ARG 0.009 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 350 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7732 (tp) cc_final: 0.7466 (tp) REVERT: C 141 ARG cc_start: 0.7873 (ttp80) cc_final: 0.7446 (ttp80) REVERT: C 268 GLU cc_start: 0.7704 (tt0) cc_final: 0.7073 (tm-30) REVERT: C 349 TYR cc_start: 0.8233 (t80) cc_final: 0.7969 (t80) REVERT: C 426 ASP cc_start: 0.7345 (t0) cc_final: 0.6991 (t70) REVERT: C 457 VAL cc_start: 0.8430 (m) cc_final: 0.8150 (p) REVERT: C 526 LYS cc_start: 0.8362 (ttpp) cc_final: 0.8142 (tttm) REVERT: C 541 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7119 (mm-30) REVERT: C 552 LYS cc_start: 0.8100 (mmtp) cc_final: 0.7773 (mmtp) REVERT: C 677 MET cc_start: 0.6616 (mmm) cc_final: 0.6371 (mmm) REVERT: C 699 ASN cc_start: 0.7302 (p0) cc_final: 0.6756 (p0) REVERT: C 719 ASP cc_start: 0.7971 (t70) cc_final: 0.7626 (t0) REVERT: C 793 ILE cc_start: 0.8483 (mt) cc_final: 0.8088 (mt) REVERT: B 19 LEU cc_start: 0.7887 (tp) cc_final: 0.7576 (tp) REVERT: B 93 THR cc_start: 0.7534 (OUTLIER) cc_final: 0.7137 (p) REVERT: B 136 ARG cc_start: 0.8043 (ttt90) cc_final: 0.7793 (ttm-80) REVERT: A 134 TYR cc_start: 0.7826 (m-10) cc_final: 0.7169 (m-10) REVERT: A 140 CYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7268 (t) REVERT: A 235 ASP cc_start: 0.7066 (OUTLIER) cc_final: 0.6273 (p0) REVERT: A 268 GLU cc_start: 0.7593 (tt0) cc_final: 0.6990 (tm-30) REVERT: A 275 ASN cc_start: 0.8356 (t0) cc_final: 0.8096 (t0) REVERT: A 291 MET cc_start: 0.7349 (mmm) cc_final: 0.6935 (mmm) REVERT: A 300 GLU cc_start: 0.7741 (pt0) cc_final: 0.7499 (pt0) REVERT: A 349 TYR cc_start: 0.8158 (t80) cc_final: 0.7866 (t80) REVERT: A 426 ASP cc_start: 0.7253 (t0) cc_final: 0.6911 (t70) REVERT: A 429 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6744 (tt0) REVERT: A 457 VAL cc_start: 0.8578 (m) cc_final: 0.8091 (p) REVERT: A 459 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6907 (mm-30) REVERT: A 525 LEU cc_start: 0.8633 (mt) cc_final: 0.8403 (mp) REVERT: A 526 LYS cc_start: 0.8352 (ttpp) cc_final: 0.8139 (ttpp) REVERT: A 552 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7851 (mttp) REVERT: A 635 MET cc_start: 0.8188 (tpp) cc_final: 0.7883 (tpp) REVERT: A 667 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7421 (mt-10) REVERT: A 699 ASN cc_start: 0.7395 (p0) cc_final: 0.7041 (p0) REVERT: A 712 GLU cc_start: 0.7513 (tt0) cc_final: 0.7141 (tt0) REVERT: A 747 LYS cc_start: 0.8474 (mttm) cc_final: 0.8243 (mmmt) REVERT: A 793 ILE cc_start: 0.8467 (mt) cc_final: 0.8126 (mt) outliers start: 40 outliers final: 30 residues processed: 373 average time/residue: 0.3490 time to fit residues: 173.5506 Evaluate side-chains 379 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 345 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 545 MET Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 825 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN C 335 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 335 GLN A 684 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13948 Z= 0.244 Angle : 0.496 10.667 18832 Z= 0.250 Chirality : 0.040 0.134 2060 Planarity : 0.003 0.035 2442 Dihedral : 3.721 17.178 1846 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.55 % Allowed : 23.69 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.21), residues: 1648 helix: 0.94 (0.18), residues: 888 sheet: -0.76 (0.69), residues: 68 loop : 0.12 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 139 HIS 0.003 0.001 HIS C 655 PHE 0.023 0.001 PHE C 475 TYR 0.015 0.001 TYR A 556 ARG 0.009 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 356 time to evaluate : 1.556 Fit side-chains revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7729 (tp) cc_final: 0.7435 (tp) REVERT: D 62 ARG cc_start: 0.7689 (mtt-85) cc_final: 0.7378 (mtt90) REVERT: C 138 GLU cc_start: 0.7317 (tp30) cc_final: 0.7080 (tp30) REVERT: C 141 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7446 (ttp80) REVERT: C 241 ARG cc_start: 0.7976 (ptp90) cc_final: 0.7500 (mtm110) REVERT: C 268 GLU cc_start: 0.7716 (tt0) cc_final: 0.7079 (tm-30) REVERT: C 426 ASP cc_start: 0.7328 (t0) cc_final: 0.6992 (t70) REVERT: C 457 VAL cc_start: 0.8459 (m) cc_final: 0.8163 (p) REVERT: C 552 LYS cc_start: 0.8077 (mmtp) cc_final: 0.7744 (mmtp) REVERT: C 677 MET cc_start: 0.6742 (mmm) cc_final: 0.6519 (mmm) REVERT: C 699 ASN cc_start: 0.7258 (p0) cc_final: 0.6685 (p0) REVERT: C 719 ASP cc_start: 0.7984 (t70) cc_final: 0.7615 (t0) REVERT: C 793 ILE cc_start: 0.8496 (mt) cc_final: 0.8130 (mt) REVERT: B 19 LEU cc_start: 0.7890 (tp) cc_final: 0.7565 (tp) REVERT: B 93 THR cc_start: 0.7521 (OUTLIER) cc_final: 0.7127 (p) REVERT: A 134 TYR cc_start: 0.7846 (m-10) cc_final: 0.7214 (m-10) REVERT: A 140 CYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7284 (t) REVERT: A 235 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6327 (p0) REVERT: A 268 GLU cc_start: 0.7592 (tt0) cc_final: 0.6980 (tm-30) REVERT: A 275 ASN cc_start: 0.8351 (t0) cc_final: 0.8083 (t0) REVERT: A 291 MET cc_start: 0.7323 (mmm) cc_final: 0.6895 (mmm) REVERT: A 300 GLU cc_start: 0.7767 (pt0) cc_final: 0.7520 (pt0) REVERT: A 349 TYR cc_start: 0.8126 (t80) cc_final: 0.7851 (t80) REVERT: A 426 ASP cc_start: 0.7243 (t0) cc_final: 0.6910 (t70) REVERT: A 429 GLU cc_start: 0.7006 (mt-10) cc_final: 0.6749 (tt0) REVERT: A 457 VAL cc_start: 0.8559 (m) cc_final: 0.8065 (p) REVERT: A 459 GLU cc_start: 0.7215 (mm-30) cc_final: 0.6921 (mm-30) REVERT: A 552 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7854 (mttp) REVERT: A 667 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7416 (mt-10) REVERT: A 699 ASN cc_start: 0.7461 (p0) cc_final: 0.7104 (p0) REVERT: A 712 GLU cc_start: 0.7527 (tt0) cc_final: 0.7142 (tt0) REVERT: A 747 LYS cc_start: 0.8463 (mttm) cc_final: 0.8232 (mmmt) REVERT: A 793 ILE cc_start: 0.8485 (mt) cc_final: 0.8177 (mt) outliers start: 39 outliers final: 27 residues processed: 380 average time/residue: 0.3387 time to fit residues: 171.8530 Evaluate side-chains 382 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 351 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 724 LYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.5980 chunk 151 optimal weight: 1.9990 chunk 138 optimal weight: 0.0070 chunk 147 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 146 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13948 Z= 0.187 Angle : 0.480 11.056 18832 Z= 0.241 Chirality : 0.039 0.142 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.622 16.410 1846 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.42 % Allowed : 23.83 % Favored : 73.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1648 helix: 1.07 (0.18), residues: 890 sheet: -0.81 (0.68), residues: 68 loop : 0.16 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.002 0.000 HIS C 655 PHE 0.021 0.001 PHE A 475 TYR 0.016 0.001 TYR A 694 ARG 0.008 0.000 ARG B 62 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 350 time to evaluate : 1.639 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7721 (tp) cc_final: 0.7453 (tp) REVERT: D 62 ARG cc_start: 0.7671 (mtt-85) cc_final: 0.7396 (mtt90) REVERT: D 124 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7615 (ttp-110) REVERT: C 138 GLU cc_start: 0.7347 (tp30) cc_final: 0.7095 (tp30) REVERT: C 140 CYS cc_start: 0.7241 (OUTLIER) cc_final: 0.7031 (t) REVERT: C 141 ARG cc_start: 0.7889 (ttp80) cc_final: 0.7441 (ttp80) REVERT: C 165 GLN cc_start: 0.8134 (mp10) cc_final: 0.7797 (mp10) REVERT: C 241 ARG cc_start: 0.7950 (ptp90) cc_final: 0.7449 (mtm110) REVERT: C 268 GLU cc_start: 0.7709 (tt0) cc_final: 0.7072 (tm-30) REVERT: C 304 MET cc_start: 0.6859 (tpp) cc_final: 0.6635 (mmm) REVERT: C 349 TYR cc_start: 0.8242 (t80) cc_final: 0.7974 (t80) REVERT: C 426 ASP cc_start: 0.7307 (t0) cc_final: 0.6970 (t70) REVERT: C 457 VAL cc_start: 0.8449 (m) cc_final: 0.8156 (p) REVERT: C 526 LYS cc_start: 0.8364 (ttpp) cc_final: 0.8151 (ttpp) REVERT: C 552 LYS cc_start: 0.8070 (mmtp) cc_final: 0.7740 (mmtp) REVERT: C 677 MET cc_start: 0.6759 (mmm) cc_final: 0.6528 (mmm) REVERT: C 699 ASN cc_start: 0.7251 (p0) cc_final: 0.6683 (p0) REVERT: C 719 ASP cc_start: 0.7946 (t70) cc_final: 0.7596 (t0) REVERT: C 735 ARG cc_start: 0.8471 (ttp80) cc_final: 0.8259 (ttt-90) REVERT: C 793 ILE cc_start: 0.8477 (mt) cc_final: 0.8108 (mt) REVERT: B 19 LEU cc_start: 0.7857 (tp) cc_final: 0.7539 (tp) REVERT: B 93 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7105 (p) REVERT: A 134 TYR cc_start: 0.7844 (m-10) cc_final: 0.7573 (m-10) REVERT: A 140 CYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7280 (t) REVERT: A 235 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6299 (p0) REVERT: A 268 GLU cc_start: 0.7557 (tt0) cc_final: 0.7046 (tm-30) REVERT: A 275 ASN cc_start: 0.8410 (t0) cc_final: 0.8111 (t0) REVERT: A 291 MET cc_start: 0.7262 (mmm) cc_final: 0.6833 (mmm) REVERT: A 300 GLU cc_start: 0.7766 (pt0) cc_final: 0.7515 (pt0) REVERT: A 349 TYR cc_start: 0.8120 (t80) cc_final: 0.7816 (t80) REVERT: A 426 ASP cc_start: 0.7223 (t0) cc_final: 0.6901 (t70) REVERT: A 429 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6786 (tt0) REVERT: A 459 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6884 (mm-30) REVERT: A 552 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7859 (mttp) REVERT: A 667 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7446 (mt-10) REVERT: A 699 ASN cc_start: 0.7454 (p0) cc_final: 0.7101 (p0) REVERT: A 712 GLU cc_start: 0.7506 (tt0) cc_final: 0.7140 (tt0) REVERT: A 747 LYS cc_start: 0.8446 (mttm) cc_final: 0.8215 (mmmt) REVERT: A 793 ILE cc_start: 0.8483 (mt) cc_final: 0.8181 (mt) outliers start: 37 outliers final: 28 residues processed: 374 average time/residue: 0.3428 time to fit residues: 170.6702 Evaluate side-chains 379 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 345 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 693 MET Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 747 LYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 0.0570 chunk 155 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 163 optimal weight: 0.4980 chunk 150 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13948 Z= 0.199 Angle : 0.488 11.602 18832 Z= 0.245 Chirality : 0.039 0.152 2060 Planarity : 0.003 0.036 2442 Dihedral : 3.637 16.584 1846 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.61 % Allowed : 24.09 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1648 helix: 1.07 (0.18), residues: 890 sheet: -0.85 (0.67), residues: 68 loop : 0.19 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 139 HIS 0.003 0.001 HIS C 655 PHE 0.022 0.001 PHE C 475 TYR 0.018 0.001 TYR A 694 ARG 0.008 0.000 ARG C 539 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 354 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 19 LEU cc_start: 0.7716 (tp) cc_final: 0.7446 (tp) REVERT: D 62 ARG cc_start: 0.7676 (mtt-85) cc_final: 0.7407 (mtt90) REVERT: D 124 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7607 (ttp-110) REVERT: C 134 TYR cc_start: 0.7825 (m-10) cc_final: 0.7594 (m-80) REVERT: C 140 CYS cc_start: 0.7260 (OUTLIER) cc_final: 0.7037 (t) REVERT: C 141 ARG cc_start: 0.7899 (ttp80) cc_final: 0.7460 (ttp80) REVERT: C 165 GLN cc_start: 0.8128 (mp10) cc_final: 0.7793 (mp10) REVERT: C 241 ARG cc_start: 0.7913 (ptp90) cc_final: 0.7430 (mtm110) REVERT: C 268 GLU cc_start: 0.7704 (tt0) cc_final: 0.7073 (tm-30) REVERT: C 349 TYR cc_start: 0.8245 (t80) cc_final: 0.7980 (t80) REVERT: C 426 ASP cc_start: 0.7287 (t0) cc_final: 0.6960 (t70) REVERT: C 457 VAL cc_start: 0.8437 (m) cc_final: 0.8214 (p) REVERT: C 459 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6894 (mp0) REVERT: C 478 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7635 (mtp) REVERT: C 552 LYS cc_start: 0.8067 (mmtp) cc_final: 0.7735 (mmtp) REVERT: C 677 MET cc_start: 0.6727 (mmm) cc_final: 0.6472 (mmm) REVERT: C 699 ASN cc_start: 0.7274 (p0) cc_final: 0.6702 (p0) REVERT: C 719 ASP cc_start: 0.7938 (t70) cc_final: 0.7590 (t0) REVERT: C 735 ARG cc_start: 0.8482 (ttp80) cc_final: 0.8269 (ttt-90) REVERT: C 793 ILE cc_start: 0.8479 (mt) cc_final: 0.8113 (mt) REVERT: B 19 LEU cc_start: 0.7854 (tp) cc_final: 0.7528 (tp) REVERT: B 93 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7106 (p) REVERT: A 134 TYR cc_start: 0.7859 (m-10) cc_final: 0.7585 (m-10) REVERT: A 140 CYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7290 (t) REVERT: A 235 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6318 (p0) REVERT: A 268 GLU cc_start: 0.7522 (tt0) cc_final: 0.7044 (tm-30) REVERT: A 275 ASN cc_start: 0.8402 (t0) cc_final: 0.8119 (t0) REVERT: A 291 MET cc_start: 0.7274 (mmm) cc_final: 0.6831 (mmm) REVERT: A 300 GLU cc_start: 0.7773 (pt0) cc_final: 0.7530 (pt0) REVERT: A 349 TYR cc_start: 0.8121 (t80) cc_final: 0.7826 (t80) REVERT: A 426 ASP cc_start: 0.7224 (t0) cc_final: 0.6901 (t70) REVERT: A 429 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6759 (tt0) REVERT: A 457 VAL cc_start: 0.8535 (m) cc_final: 0.8083 (p) REVERT: A 459 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6900 (mm-30) REVERT: A 552 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7843 (mttp) REVERT: A 667 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7445 (mt-10) REVERT: A 699 ASN cc_start: 0.7460 (p0) cc_final: 0.7119 (p0) REVERT: A 712 GLU cc_start: 0.7520 (tt0) cc_final: 0.7141 (tt0) REVERT: A 747 LYS cc_start: 0.8437 (mttm) cc_final: 0.8204 (mmmt) REVERT: A 793 ILE cc_start: 0.8478 (mt) cc_final: 0.8191 (mt) outliers start: 40 outliers final: 31 residues processed: 380 average time/residue: 0.3480 time to fit residues: 177.3124 Evaluate side-chains 387 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 349 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 105 ASP Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 124 ARG Chi-restraints excluded: chain C residue 140 CYS Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain C residue 394 GLU Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain C residue 478 MET Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 570 VAL Chi-restraints excluded: chain C residue 654 SER Chi-restraints excluded: chain C residue 743 GLU Chi-restraints excluded: chain C residue 747 LYS Chi-restraints excluded: chain C residue 760 CYS Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 101 LYS Chi-restraints excluded: chain B residue 105 ASP Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain A residue 140 CYS Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 491 LEU Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 570 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 728 LYS Chi-restraints excluded: chain A residue 742 ASN Chi-restraints excluded: chain A residue 760 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 0.6980 chunk 138 optimal weight: 0.2980 chunk 39 optimal weight: 0.8980 chunk 119 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 16 optimal weight: 0.0870 chunk 24 optimal weight: 0.5980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 321 GLN ** C 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.141290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.119237 restraints weight = 19256.233| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.28 r_work: 0.3304 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13948 Z= 0.160 Angle : 0.475 11.808 18832 Z= 0.238 Chirality : 0.039 0.147 2060 Planarity : 0.003 0.037 2442 Dihedral : 3.546 15.563 1846 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.35 % Allowed : 24.48 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.21), residues: 1648 helix: 1.10 (0.18), residues: 900 sheet: -1.08 (0.64), residues: 72 loop : 0.21 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 600 HIS 0.002 0.000 HIS C 655 PHE 0.022 0.001 PHE C 475 TYR 0.021 0.001 TYR A 694 ARG 0.008 0.000 ARG B 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4001.34 seconds wall clock time: 70 minutes 60.00 seconds (4260.00 seconds total)