Starting phenix.real_space_refine on Thu Jul 2 22:47:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jcz_36170/07_2026/8jcz_36170.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcz_36170/07_2026/8jcz_36170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jcz_36170/07_2026/8jcz_36170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcz_36170/07_2026/8jcz_36170.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8jcz_36170/07_2026/8jcz_36170.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jcz_36170/07_2026/8jcz_36170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jcz_36170/07_2026/8jcz_36170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcz_36170/07_2026/8jcz_36170.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 6631 2.51 5 N 1843 2.21 5 O 2001 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10540 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5237 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 184} Link IDs: {'PTRANS': 37, 'TRANS': 723} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 722 Unresolved non-hydrogen angles: 930 Unresolved non-hydrogen dihedrals: 598 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'ARG:plan': 19, 'ASP:plan': 7, 'GLU:plan': 16, 'ASN:plan1': 8, 'GLN:plan1': 7, 'TYR:plan': 10, 'TRP:plan': 3, 'PHE:plan': 13, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 422 Chain: "3" Number of atoms: 5223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 743, 5223 Classifications: {'peptide': 743} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 28, 'TRANS': 714} Chain breaks: 4 Unresolved non-hydrogen bonds: 692 Unresolved non-hydrogen angles: 882 Unresolved non-hydrogen dihedrals: 592 Unresolved non-hydrogen chiralities: 56 Planarities with less than four sites: {'ARG:plan': 15, 'GLU:plan': 11, 'GLN:plan1': 7, 'ASN:plan1': 10, 'HIS:plan': 3, 'ASP:plan': 9, 'TRP:plan': 4, 'TYR:plan': 10, 'PHE:plan': 13} Unresolved non-hydrogen planarities: 401 Chain: "2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.15, per 1000 atoms: 0.20 Number of scatterers: 10540 At special positions: 0 Unit cell: (88.893, 121.023, 183.141, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2001 8.00 N 1843 7.00 C 6631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 240 " - pdb=" SG CYS 3 527 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG 22001 " - " ASN 2 203 " " NAG 32001 " - " ASN 3 209 " Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 533.2 milliseconds 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2818 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 48.1% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain '2' and resid 59 through 74 Processing helix chain '2' and resid 94 through 108 removed outlier: 4.034A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL 2 106 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) Processing helix chain '2' and resid 144 through 158 removed outlier: 4.170A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE 2 158 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) Processing helix chain '2' and resid 169 through 173 removed outlier: 3.724A pdb=" N LEU 2 172 " --> pdb=" O SER 2 169 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER 2 173 " --> pdb=" O ALA 2 170 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 169 through 173' Processing helix chain '2' and resid 188 through 202 removed outlier: 4.011A pdb=" N ALA 2 192 " --> pdb=" O ASP 2 188 " (cutoff:3.500A) Processing helix chain '2' and resid 214 through 231 removed outlier: 3.538A pdb=" N GLU 2 218 " --> pdb=" O GLY 2 214 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY 2 220 " --> pdb=" O TYR 2 216 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ILE 2 221 " --> pdb=" O GLY 2 217 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU 2 222 " --> pdb=" O GLU 2 218 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA 2 223 " --> pdb=" O THR 2 219 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 259 Processing helix chain '2' and resid 271 through 286 Processing helix chain '2' and resid 324 through 333 Processing helix chain '2' and resid 344 through 353 Processing helix chain '2' and resid 377 through 400 removed outlier: 3.813A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 377 " (cutoff:3.500A) Processing helix chain '2' and resid 414 through 422 Processing helix chain '2' and resid 565 through 567 No H-bonds generated for 'chain '2' and resid 565 through 567' Processing helix chain '2' and resid 568 through 594 removed outlier: 3.583A pdb=" N VAL 2 572 " --> pdb=" O ALA 2 568 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ALA 2 594 " --> pdb=" O VAL 2 590 " (cutoff:3.500A) Processing helix chain '2' and resid 603 through 626 removed outlier: 3.849A pdb=" N TYR 2 607 " --> pdb=" O ARG 2 603 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS 2 626 " --> pdb=" O ILE 2 622 " (cutoff:3.500A) Processing helix chain '2' and resid 632 through 660 removed outlier: 3.535A pdb=" N GLY 2 640 " --> pdb=" O ARG 2 636 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE 2 660 " --> pdb=" O ARG 2 656 " (cutoff:3.500A) Processing helix chain '2' and resid 677 through 701 Processing helix chain '2' and resid 726 through 750 removed outlier: 3.522A pdb=" N GLY 2 730 " --> pdb=" O ALA 2 726 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER 2 731 " --> pdb=" O SER 2 727 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N LYS 2 748 " --> pdb=" O LEU 2 744 " (cutoff:3.500A) Processing helix chain '2' and resid 755 through 784 Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 786 through 819 removed outlier: 4.178A pdb=" N THR 2 791 " --> pdb=" O TYR 2 787 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N THR 2 792 " --> pdb=" O ARG 2 788 " (cutoff:3.500A) Proline residue: 2 812 - end of helix removed outlier: 3.932A pdb=" N HIS 2 815 " --> pdb=" O ALA 2 811 " (cutoff:3.500A) Processing helix chain '3' and resid 65 through 82 Processing helix chain '3' and resid 101 through 110 Processing helix chain '3' and resid 150 through 164 removed outlier: 4.253A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE 3 164 " --> pdb=" O LEU 3 160 " (cutoff:3.500A) Processing helix chain '3' and resid 175 through 180 removed outlier: 3.543A pdb=" N LEU 3 178 " --> pdb=" O SER 3 175 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP 3 180 " --> pdb=" O LYS 3 177 " (cutoff:3.500A) Processing helix chain '3' and resid 194 through 208 removed outlier: 3.929A pdb=" N ALA 3 198 " --> pdb=" O ASP 3 194 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA 3 202 " --> pdb=" O ALA 3 198 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLU 3 203 " --> pdb=" O LYS 3 199 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE 3 204 " --> pdb=" O ALA 3 200 " (cutoff:3.500A) Processing helix chain '3' and resid 221 through 237 removed outlier: 4.052A pdb=" N THR 3 225 " --> pdb=" O ASP 3 221 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY 3 226 " --> pdb=" O TYR 3 222 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU 3 228 " --> pdb=" O GLU 3 224 " (cutoff:3.500A) Processing helix chain '3' and resid 252 through 265 Processing helix chain '3' and resid 277 through 292 removed outlier: 3.600A pdb=" N ARG 3 290 " --> pdb=" O ALA 3 286 " (cutoff:3.500A) Processing helix chain '3' and resid 313 through 318 removed outlier: 3.621A pdb=" N ALA 3 317 " --> pdb=" O SER 3 313 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR 3 318 " --> pdb=" O GLU 3 314 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 313 through 318' Processing helix chain '3' and resid 330 through 339 removed outlier: 3.528A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 359 Processing helix chain '3' and resid 387 through 389 No H-bonds generated for 'chain '3' and resid 387 through 389' Processing helix chain '3' and resid 390 through 412 removed outlier: 3.792A pdb=" N ALA 3 403 " --> pdb=" O ALA 3 399 " (cutoff:3.500A) Processing helix chain '3' and resid 419 through 423 Processing helix chain '3' and resid 426 through 434 Processing helix chain '3' and resid 493 through 497 Processing helix chain '3' and resid 574 through 598 removed outlier: 4.322A pdb=" N GLY 3 579 " --> pdb=" O ALA 3 575 " (cutoff:3.500A) Proline residue: 3 580 - end of helix Processing helix chain '3' and resid 612 through 633 removed outlier: 3.795A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) Processing helix chain '3' and resid 641 through 665 removed outlier: 4.448A pdb=" N ARG 3 645 " --> pdb=" O CYS 3 641 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS 3 662 " --> pdb=" O ALA 3 658 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS 3 665 " --> pdb=" O THR 3 661 " (cutoff:3.500A) Processing helix chain '3' and resid 685 through 708 removed outlier: 3.654A pdb=" N LEU 3 693 " --> pdb=" O VAL 3 689 " (cutoff:3.500A) Processing helix chain '3' and resid 720 through 724 Processing helix chain '3' and resid 737 through 758 removed outlier: 3.796A pdb=" N THR 3 758 " --> pdb=" O TYR 3 754 " (cutoff:3.500A) Processing helix chain '3' and resid 768 through 792 Proline residue: 3 787 - end of helix removed outlier: 3.985A pdb=" N TYR 3 790 " --> pdb=" O LEU 3 786 " (cutoff:3.500A) Processing helix chain '3' and resid 796 through 825 removed outlier: 4.242A pdb=" N THR 3 800 " --> pdb=" O TYR 3 796 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 25 through 28 removed outlier: 4.185A pdb=" N GLY 2 36 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL 2 33 " --> pdb=" O ILE 2 136 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY 2 138 " --> pdb=" O VAL 2 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 41 through 43 Processing sheet with id=AA3, first strand: chain '2' and resid 162 through 164 Processing sheet with id=AA4, first strand: chain '2' and resid 206 through 207 Processing sheet with id=AA5, first strand: chain '2' and resid 240 through 241 removed outlier: 6.866A pdb=" N ALA 2 211 " --> pdb=" O VAL 2 241 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER 2 212 " --> pdb=" O PHE 2 269 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALA 2 266 " --> pdb=" O VAL 2 292 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '2' and resid 314 through 319 removed outlier: 4.222A pdb=" N ALA 2 314 " --> pdb=" O TYR 2 458 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TYR 2 453 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N TYR 2 473 " --> pdb=" O TYR 2 453 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE 2 455 " --> pdb=" O VAL 2 471 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 428 through 429 removed outlier: 4.133A pdb=" N PHE 2 428 " --> pdb=" O VAL 2 441 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '2' and resid 507 through 513 removed outlier: 6.007A pdb=" N ASN 2 507 " --> pdb=" O CYS 2 522 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS 2 522 " --> pdb=" O ASN 2 507 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N VAL 2 509 " --> pdb=" O TRP 2 520 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N TRP 2 520 " --> pdb=" O VAL 2 509 " (cutoff:3.500A) removed outlier: 10.535A pdb=" N SER 2 511 " --> pdb=" O CYS 2 518 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N CYS 2 518 " --> pdb=" O SER 2 511 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN 2 513 " --> pdb=" O GLU 2 516 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '2' and resid 530 through 531 Processing sheet with id=AB1, first strand: chain '3' and resid 33 through 35 removed outlier: 6.480A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL 3 40 " --> pdb=" O ILE 3 142 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY 3 144 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N ILE 3 169 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL 3 145 " --> pdb=" O ILE 3 169 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 48 through 50 removed outlier: 5.196A pdb=" N GLU 3 49 " --> pdb=" O GLY 3 58 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '3' and resid 240 through 244 removed outlier: 7.954A pdb=" N VAL 3 213 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ALA 3 244 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR 3 215 " --> pdb=" O ALA 3 244 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL 3 271 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL 3 272 " --> pdb=" O VAL 3 298 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TRP 3 297 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N LEU 3 323 " --> pdb=" O TRP 3 297 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ALA 3 299 " --> pdb=" O LEU 3 323 " (cutoff:3.500A) removed outlier: 9.271A pdb=" N LEU 3 325 " --> pdb=" O ALA 3 299 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR 3 466 " --> pdb=" O HIS 3 485 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N HIS 3 485 " --> pdb=" O TYR 3 466 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL 3 468 " --> pdb=" O VAL 3 483 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1581 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: 1.58 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2949 1.33 - 1.46: 2006 1.46 - 1.58: 5720 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 10755 Sorted by residual: bond pdb=" CAT Z99 22002 " pdb=" OAP Z99 22002 " ideal model delta sigma weight residual 1.364 1.455 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" CAT Z99 32002 " pdb=" OAP Z99 32002 " ideal model delta sigma weight residual 1.364 1.453 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" CAS Z99 32002 " pdb=" OAP Z99 32002 " ideal model delta sigma weight residual 1.369 1.452 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" CAS Z99 22002 " pdb=" OAP Z99 22002 " ideal model delta sigma weight residual 1.369 1.451 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" CA PRO 3 192 " pdb=" C PRO 3 192 " ideal model delta sigma weight residual 1.517 1.537 -0.020 6.70e-03 2.23e+04 8.52e+00 ... (remaining 10750 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 14463 1.85 - 3.71: 188 3.71 - 5.56: 45 5.56 - 7.42: 8 7.42 - 9.27: 7 Bond angle restraints: 14711 Sorted by residual: angle pdb=" CAX Z99 22002 " pdb=" CAZ Z99 22002 " pdb=" CAY Z99 22002 " ideal model delta sigma weight residual 120.67 111.40 9.27 3.00e+00 1.11e-01 9.55e+00 angle pdb=" O PRO 3 192 " pdb=" C PRO 3 192 " pdb=" N PRO 3 193 " ideal model delta sigma weight residual 121.15 122.60 -1.45 4.70e-01 4.53e+00 9.46e+00 angle pdb=" CAX Z99 32002 " pdb=" CAZ Z99 32002 " pdb=" CAY Z99 32002 " ideal model delta sigma weight residual 120.67 111.88 8.79 3.00e+00 1.11e-01 8.58e+00 angle pdb=" CG1 VAL 3 504 " pdb=" CB VAL 3 504 " pdb=" CG2 VAL 3 504 " ideal model delta sigma weight residual 110.80 104.37 6.43 2.20e+00 2.07e-01 8.53e+00 angle pdb=" N VAL 3 474 " pdb=" CA VAL 3 474 " pdb=" C VAL 3 474 " ideal model delta sigma weight residual 108.86 104.23 4.63 1.63e+00 3.76e-01 8.07e+00 ... (remaining 14706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 5834 17.48 - 34.95: 425 34.95 - 52.43: 90 52.43 - 69.90: 15 69.90 - 87.38: 6 Dihedral angle restraints: 6370 sinusoidal: 2017 harmonic: 4353 Sorted by residual: dihedral pdb=" CB CYS 2 400 " pdb=" SG CYS 2 400 " pdb=" SG CYS 2 407 " pdb=" CB CYS 2 407 " ideal model delta sinusoidal sigma weight residual 93.00 -179.62 -87.38 1 1.00e+01 1.00e-02 9.16e+01 dihedral pdb=" CB CYS 3 57 " pdb=" SG CYS 3 57 " pdb=" SG CYS 3 99 " pdb=" CB CYS 3 99 " ideal model delta sinusoidal sigma weight residual -86.00 -158.80 72.80 1 1.00e+01 1.00e-02 6.76e+01 dihedral pdb=" CB CYS 2 525 " pdb=" SG CYS 2 525 " pdb=" SG CYS 2 537 " pdb=" CB CYS 2 537 " ideal model delta sinusoidal sigma weight residual -86.00 -23.84 -62.16 1 1.00e+01 1.00e-02 5.12e+01 ... (remaining 6367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.049: 1723 1.049 - 2.097: 0 2.097 - 3.146: 0 3.146 - 4.194: 0 4.194 - 5.243: 2 Chirality restraints: 1725 Sorted by residual: chirality pdb=" CAW Z99 32002 " pdb=" CAN Z99 32002 " pdb=" CAU Z99 32002 " pdb=" CAV Z99 32002 " both_signs ideal model delta sigma weight residual False 2.61 -2.63 5.24 2.00e-01 2.50e+01 6.87e+02 chirality pdb=" CAW Z99 22002 " pdb=" CAN Z99 22002 " pdb=" CAU Z99 22002 " pdb=" CAV Z99 22002 " both_signs ideal model delta sigma weight residual False 2.61 -2.46 5.07 2.00e-01 2.50e+01 6.43e+02 chirality pdb=" CAZ Z99 22002 " pdb=" CAO Z99 22002 " pdb=" CAX Z99 22002 " pdb=" CAY Z99 22002 " both_signs ideal model delta sigma weight residual True 2.39 -2.72 -0.33 2.00e-01 2.50e+01 2.74e+00 ... (remaining 1722 not shown) Planarity restraints: 1932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 74 " -0.201 9.50e-02 1.11e+02 8.99e-02 4.98e+00 pdb=" NE ARG 2 74 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG 2 74 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 74 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 74 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU 2 495 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.81e+00 pdb=" C LEU 2 495 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU 2 495 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO 2 496 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA 2 132 " -0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO 2 133 " 0.080 5.00e-02 4.00e+02 pdb=" CA PRO 2 133 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO 2 133 " -0.026 5.00e-02 4.00e+02 ... (remaining 1929 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2127 2.78 - 3.31: 10228 3.31 - 3.84: 17439 3.84 - 4.37: 19306 4.37 - 4.90: 33731 Nonbonded interactions: 82831 Sorted by model distance: nonbonded pdb=" O SER 3 255 " pdb=" OG SER 3 258 " model vdw 2.247 3.040 nonbonded pdb=" OG SER 2 148 " pdb=" OG SER 2 167 " model vdw 2.303 3.040 nonbonded pdb=" O LEU 3 39 " pdb=" N GLY 3 92 " model vdw 2.307 3.120 nonbonded pdb=" OD1 ASP 3 334 " pdb=" NE2 GLN 3 386 " model vdw 2.309 3.120 nonbonded pdb=" O ALA 3 658 " pdb=" OG1 THR 3 661 " model vdw 2.311 3.040 ... (remaining 82826 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 9.830 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 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 0.091 10775 Z= 0.163 Angle : 0.567 9.272 14753 Z= 0.271 Chirality : 0.181 5.243 1725 Planarity : 0.004 0.090 1930 Dihedral : 12.895 83.424 3498 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.22 % Allowed : 7.03 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.22), residues: 1486 helix: 2.13 (0.21), residues: 646 sheet: -0.64 (0.55), residues: 114 loop : -1.92 (0.21), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 445 TYR 0.023 0.001 TYR 3 256 PHE 0.008 0.001 PHE 3 195 TRP 0.006 0.001 TRP 2 297 HIS 0.004 0.001 HIS 2 77 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (10755) covalent geometry : angle 0.56676 / 0.27 (14711) SS BOND : bond 0.00128 / 0.07 ( 18) SS BOND : angle 0.65952 / 0.33 ( 36) hydrogen bonds : bond 0.13733 / 9.87 ( 541) hydrogen bonds : angle 5.68541 / 3.87 ( 1581) link_NAG-ASN : bond 0.00180 / 0.09 ( 2) link_NAG-ASN : angle 0.61144 / 0.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.300 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 96 average time/residue: 0.3805 time to fit residues: 40.4691 Evaluate side-chains 95 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 474 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.0980 chunk 149 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 42 GLN 2 374 GLN 3 386 GLN 3 472 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.235534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.154175 restraints weight = 11287.452| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 3.03 r_work: 0.3391 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10775 Z= 0.165 Angle : 0.576 12.760 14753 Z= 0.285 Chirality : 0.043 0.193 1725 Planarity : 0.004 0.036 1930 Dihedral : 4.053 54.873 1602 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.30 % Allowed : 7.14 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.22), residues: 1486 helix: 2.21 (0.20), residues: 656 sheet: -0.77 (0.48), residues: 141 loop : -1.96 (0.22), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 229 TYR 0.012 0.001 TYR 3 398 PHE 0.015 0.002 PHE 3 195 TRP 0.008 0.001 TRP 3 297 HIS 0.003 0.001 HIS 3 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (10755) covalent geometry : angle 0.57589 / 0.28 (14711) SS BOND : bond 0.00240 / 0.15 ( 18) SS BOND : angle 0.70014 / 0.37 ( 36) hydrogen bonds : bond 0.03825 / 2.52 ( 541) hydrogen bonds : angle 4.23881 / 2.92 ( 1581) link_NAG-ASN : bond 0.00095 / 0.05 ( 2) link_NAG-ASN : angle 0.93890 / 0.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.246 Fit side-chains REVERT: 2 190 PHE cc_start: 0.8556 (m-10) cc_final: 0.8328 (m-10) REVERT: 2 227 GLU cc_start: 0.6407 (mm-30) cc_final: 0.5950 (mp0) REVERT: 2 373 GLU cc_start: 0.7725 (tp30) cc_final: 0.7358 (tt0) REVERT: 2 427 LYS cc_start: 0.7738 (ttmt) cc_final: 0.7444 (ttpt) REVERT: 3 199 LYS cc_start: 0.8118 (mtpp) cc_final: 0.7210 (mptp) REVERT: 3 201 MET cc_start: 0.7889 (ptt) cc_final: 0.7621 (ptt) REVERT: 3 334 ASP cc_start: 0.7782 (m-30) cc_final: 0.7538 (m-30) REVERT: 3 434 TYR cc_start: 0.8575 (m-80) cc_final: 0.7485 (m-80) REVERT: 3 493 ASP cc_start: 0.7692 (t0) cc_final: 0.7213 (t0) outliers start: 12 outliers final: 4 residues processed: 111 average time/residue: 0.4201 time to fit residues: 51.1193 Evaluate side-chains 95 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 259 GLN Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 3 residue 481 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 62 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 30.0000 chunk 110 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 72 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 42 GLN 3 345 ASN 3 386 GLN 3 472 GLN 3 473 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.229563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144195 restraints weight = 11177.457| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.54 r_work: 0.3324 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 10775 Z= 0.351 Angle : 0.703 9.677 14753 Z= 0.358 Chirality : 0.049 0.219 1725 Planarity : 0.005 0.039 1930 Dihedral : 4.658 57.801 1601 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.16 % Allowed : 9.84 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.22), residues: 1486 helix: 1.75 (0.20), residues: 666 sheet: -1.46 (0.45), residues: 137 loop : -2.25 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 229 TYR 0.015 0.002 TYR 3 478 PHE 0.018 0.003 PHE 3 195 TRP 0.017 0.002 TRP 3 303 HIS 0.006 0.002 HIS 3 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00868 / 0.35 (10755) covalent geometry : angle 0.70202 / 0.36 (14711) SS BOND : bond 0.00301 / 0.19 ( 18) SS BOND : angle 0.91102 / 0.48 ( 36) hydrogen bonds : bond 0.04769 / 3.18 ( 541) hydrogen bonds : angle 4.42021 / 3.04 ( 1581) link_NAG-ASN : bond 0.00188 / 0.10 ( 2) link_NAG-ASN : angle 1.01118 / 0.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.375 Fit side-chains REVERT: 2 100 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7656 (mp0) REVERT: 2 373 GLU cc_start: 0.7993 (tp30) cc_final: 0.7680 (tt0) REVERT: 2 375 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.6532 (tm-30) REVERT: 2 414 ASN cc_start: 0.7692 (t0) cc_final: 0.7234 (t0) REVERT: 2 427 LYS cc_start: 0.8079 (ttmt) cc_final: 0.7781 (ttpt) REVERT: 3 227 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7536 (tp) REVERT: 3 334 ASP cc_start: 0.7612 (m-30) cc_final: 0.7373 (m-30) REVERT: 3 434 TYR cc_start: 0.8633 (m-80) cc_final: 0.7664 (m-80) REVERT: 3 493 ASP cc_start: 0.7894 (t70) cc_final: 0.7409 (t0) outliers start: 20 outliers final: 4 residues processed: 115 average time/residue: 0.4380 time to fit residues: 55.0854 Evaluate side-chains 96 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 259 GLN Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 227 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 30.0000 chunk 47 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 40 optimal weight: 0.9980 chunk 113 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 49 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 19 optimal weight: 0.0470 chunk 122 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 overall best weight: 2.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 42 GLN 3 472 GLN 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.225485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.138125 restraints weight = 11259.935| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.05 r_work: 0.3255 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.107 10775 Z= 0.416 Angle : 0.769 10.696 14753 Z= 0.391 Chirality : 0.051 0.196 1725 Planarity : 0.005 0.048 1930 Dihedral : 5.054 57.633 1601 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.14 % Allowed : 14.16 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1486 helix: 1.43 (0.20), residues: 669 sheet: -1.70 (0.42), residues: 146 loop : -2.49 (0.21), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG 2 83 TYR 0.021 0.003 TYR 2 180 PHE 0.018 0.003 PHE 3 440 TRP 0.017 0.003 TRP 3 303 HIS 0.007 0.002 HIS 3 485 Details of bonding type rmsd/Z covalent geometry : bond 0.01015 / 0.42 (10755) covalent geometry : angle 0.76794 / 0.39 (14711) SS BOND : bond 0.00386 / 0.24 ( 18) SS BOND : angle 0.99089 / 0.52 ( 36) hydrogen bonds : bond 0.05069 / 3.40 ( 541) hydrogen bonds : angle 4.54776 / 3.12 ( 1581) link_NAG-ASN : bond 0.00337 / 0.17 ( 2) link_NAG-ASN : angle 1.07277 / 0.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.329 Fit side-chains REVERT: 2 29 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6533 (mt-10) REVERT: 2 100 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7739 (mp0) REVERT: 2 140 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8762 (mm) REVERT: 2 227 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6731 (mp0) REVERT: 2 240 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.8081 (ptmt) REVERT: 2 373 GLU cc_start: 0.8113 (tp30) cc_final: 0.7826 (tt0) REVERT: 2 375 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.6573 (tm-30) REVERT: 2 414 ASN cc_start: 0.8030 (t0) cc_final: 0.7589 (t0) REVERT: 2 427 LYS cc_start: 0.8137 (ttmt) cc_final: 0.7858 (ttpt) REVERT: 2 439 ASN cc_start: 0.7078 (m110) cc_final: 0.6747 (p0) REVERT: 3 227 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8231 (tp) REVERT: 3 334 ASP cc_start: 0.7662 (m-30) cc_final: 0.7427 (m-30) REVERT: 3 493 ASP cc_start: 0.8051 (t70) cc_final: 0.7468 (t0) outliers start: 29 outliers final: 9 residues processed: 120 average time/residue: 0.4178 time to fit residues: 55.0292 Evaluate side-chains 107 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 29 GLU Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 140 ILE Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 240 LYS Chi-restraints excluded: chain 2 residue 259 GLN Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 481 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 0.6980 chunk 136 optimal weight: 20.0000 chunk 71 optimal weight: 40.0000 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 104 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 39 optimal weight: 0.7980 chunk 19 optimal weight: 0.0770 chunk 142 optimal weight: 6.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 42 GLN 3 473 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.230139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.141791 restraints weight = 11174.284| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 3.08 r_work: 0.3340 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10775 Z= 0.142 Angle : 0.541 6.668 14753 Z= 0.278 Chirality : 0.042 0.175 1725 Planarity : 0.004 0.040 1930 Dihedral : 4.522 57.290 1601 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.05 % Allowed : 15.68 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.22), residues: 1486 helix: 1.73 (0.20), residues: 668 sheet: -1.73 (0.41), residues: 164 loop : -2.35 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 235 TYR 0.017 0.001 TYR 2 473 PHE 0.017 0.001 PHE 2 327 TRP 0.012 0.001 TRP 2 487 HIS 0.003 0.001 HIS 3 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (10755) covalent geometry : angle 0.54075 / 0.28 (14711) SS BOND : bond 0.00208 / 0.11 ( 18) SS BOND : angle 0.59516 / 0.30 ( 36) hydrogen bonds : bond 0.03759 / 2.51 ( 541) hydrogen bonds : angle 4.17019 / 2.85 ( 1581) link_NAG-ASN : bond 0.00083 / 0.04 ( 2) link_NAG-ASN : angle 1.05245 / 0.45 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.377 Fit side-chains REVERT: 2 43 LYS cc_start: 0.7946 (ttpp) cc_final: 0.7643 (tttt) REVERT: 2 100 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7492 (mp0) REVERT: 2 285 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7710 (mt) REVERT: 2 373 GLU cc_start: 0.8055 (tp30) cc_final: 0.7754 (tt0) REVERT: 2 375 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.6403 (tm-30) REVERT: 2 414 ASN cc_start: 0.7900 (t0) cc_final: 0.7496 (t0) REVERT: 2 427 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7782 (ttpt) REVERT: 2 439 ASN cc_start: 0.7000 (m110) cc_final: 0.6717 (p0) REVERT: 2 445 ARG cc_start: 0.7814 (mpp-170) cc_final: 0.7589 (mpp-170) REVERT: 3 219 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6898 (pm20) REVERT: 3 334 ASP cc_start: 0.7618 (m-30) cc_final: 0.7393 (m-30) REVERT: 3 434 TYR cc_start: 0.8638 (m-80) cc_final: 0.7917 (m-80) REVERT: 3 493 ASP cc_start: 0.7850 (t70) cc_final: 0.7347 (t0) outliers start: 19 outliers final: 5 residues processed: 115 average time/residue: 0.3717 time to fit residues: 47.5127 Evaluate side-chains 100 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 285 LEU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 219 GLU Chi-restraints excluded: chain 3 residue 481 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 47 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 2.9990 chunk 54 optimal weight: 40.0000 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 51 optimal weight: 0.0000 chunk 137 optimal weight: 9.9990 chunk 53 optimal weight: 20.0000 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 42 GLN 2 339 ASN 2 342 ASN 3 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.227717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.136271 restraints weight = 11222.579| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.58 r_work: 0.3320 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10775 Z= 0.248 Angle : 0.625 7.472 14753 Z= 0.317 Chirality : 0.045 0.183 1725 Planarity : 0.004 0.044 1930 Dihedral : 4.682 59.821 1601 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 3.35 % Allowed : 14.59 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.22), residues: 1486 helix: 1.67 (0.20), residues: 673 sheet: -1.61 (0.42), residues: 157 loop : -2.42 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 2 229 TYR 0.024 0.002 TYR 3 318 PHE 0.013 0.002 PHE 2 348 TRP 0.012 0.002 TRP 3 303 HIS 0.005 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.25 (10755) covalent geometry : angle 0.62459 / 0.32 (14711) SS BOND : bond 0.00261 / 0.16 ( 18) SS BOND : angle 0.70874 / 0.37 ( 36) hydrogen bonds : bond 0.04229 / 2.83 ( 541) hydrogen bonds : angle 4.22797 / 2.89 ( 1581) link_NAG-ASN : bond 0.00140 / 0.07 ( 2) link_NAG-ASN : angle 0.96938 / 0.40 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 0.261 Fit side-chains REVERT: 2 43 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7625 (tttt) REVERT: 2 100 GLU cc_start: 0.7891 (mt-10) cc_final: 0.7571 (mp0) REVERT: 2 227 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6519 (mp0) REVERT: 2 269 PHE cc_start: 0.8534 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: 2 365 HIS cc_start: 0.5148 (OUTLIER) cc_final: 0.4427 (m170) REVERT: 2 373 GLU cc_start: 0.8112 (tp30) cc_final: 0.7859 (tt0) REVERT: 2 375 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.6432 (tm-30) REVERT: 2 414 ASN cc_start: 0.7947 (t0) cc_final: 0.7542 (t0) REVERT: 2 427 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7788 (ttpt) REVERT: 2 439 ASN cc_start: 0.7025 (m110) cc_final: 0.6764 (p0) REVERT: 2 445 ARG cc_start: 0.7798 (mpp-170) cc_final: 0.7575 (mpp-170) REVERT: 3 72 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7714 (ttt) REVERT: 3 228 GLU cc_start: 0.7305 (OUTLIER) cc_final: 0.6326 (mp0) REVERT: 3 232 GLN cc_start: 0.7119 (OUTLIER) cc_final: 0.6223 (mp10) REVERT: 3 334 ASP cc_start: 0.7595 (m-30) cc_final: 0.7357 (m-30) REVERT: 3 434 TYR cc_start: 0.8659 (m-80) cc_final: 0.7934 (m-80) REVERT: 3 493 ASP cc_start: 0.7918 (t70) cc_final: 0.7394 (t0) outliers start: 31 outliers final: 12 residues processed: 118 average time/residue: 0.3924 time to fit residues: 51.1934 Evaluate side-chains 111 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 43 LYS Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 134 THR Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 259 GLN Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 98 THR Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 228 GLU Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 77 optimal weight: 0.5980 chunk 90 optimal weight: 0.3980 chunk 82 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 42 GLN 2 56 HIS 2 339 ASN 3 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.229333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.140383 restraints weight = 11216.045| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 3.05 r_work: 0.3318 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10775 Z= 0.164 Angle : 0.556 6.516 14753 Z= 0.283 Chirality : 0.042 0.177 1725 Planarity : 0.004 0.040 1930 Dihedral : 4.496 58.021 1601 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 3.57 % Allowed : 14.81 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.22), residues: 1486 helix: 1.85 (0.20), residues: 667 sheet: -1.69 (0.42), residues: 165 loop : -2.33 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 229 TYR 0.025 0.002 TYR 3 318 PHE 0.012 0.001 PHE 3 195 TRP 0.009 0.001 TRP 2 349 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (10755) covalent geometry : angle 0.55556 / 0.28 (14711) SS BOND : bond 0.00206 / 0.12 ( 18) SS BOND : angle 0.58208 / 0.30 ( 36) hydrogen bonds : bond 0.03780 / 2.53 ( 541) hydrogen bonds : angle 4.05897 / 2.78 ( 1581) link_NAG-ASN : bond 0.00023 / 0.01 ( 2) link_NAG-ASN : angle 0.93095 / 0.39 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 97 time to evaluate : 0.369 Fit side-chains REVERT: 2 43 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7556 (tttt) REVERT: 2 62 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8845 (tp) REVERT: 2 100 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7544 (mp0) REVERT: 2 227 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6498 (mp0) REVERT: 2 269 PHE cc_start: 0.8507 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: 2 365 HIS cc_start: 0.5133 (OUTLIER) cc_final: 0.4385 (m170) REVERT: 2 373 GLU cc_start: 0.8149 (tp30) cc_final: 0.7908 (tt0) REVERT: 2 375 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.6404 (tm-30) REVERT: 2 414 ASN cc_start: 0.7933 (t0) cc_final: 0.7507 (t0) REVERT: 2 417 ARG cc_start: 0.8177 (ttp-170) cc_final: 0.7865 (ttm170) REVERT: 2 427 LYS cc_start: 0.8080 (ttmt) cc_final: 0.7786 (ttpt) REVERT: 2 439 ASN cc_start: 0.7115 (m110) cc_final: 0.6814 (p0) REVERT: 2 445 ARG cc_start: 0.7877 (mpp-170) cc_final: 0.7578 (mpp-170) REVERT: 3 72 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7677 (ttt) REVERT: 3 228 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6269 (mp0) REVERT: 3 232 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.6167 (mp10) REVERT: 3 251 ASN cc_start: 0.5847 (m-40) cc_final: 0.5576 (m-40) REVERT: 3 263 LEU cc_start: 0.6669 (OUTLIER) cc_final: 0.6380 (mt) REVERT: 3 334 ASP cc_start: 0.7619 (m-30) cc_final: 0.7360 (m-30) REVERT: 3 434 TYR cc_start: 0.8658 (m-80) cc_final: 0.8005 (m-80) REVERT: 3 493 ASP cc_start: 0.7852 (t70) cc_final: 0.7352 (t0) outliers start: 33 outliers final: 12 residues processed: 123 average time/residue: 0.3452 time to fit residues: 47.2276 Evaluate side-chains 119 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 43 LYS Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 134 THR Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 41 LEU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 98 THR Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 228 GLU Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 42 GLN 2 56 HIS 2 339 ASN 3 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.225060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152657 restraints weight = 11013.007| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.52 r_work: 0.3340 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10775 Z= 0.217 Angle : 0.615 12.814 14753 Z= 0.308 Chirality : 0.044 0.181 1725 Planarity : 0.004 0.040 1930 Dihedral : 4.605 59.153 1601 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 3.03 % Allowed : 16.43 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.22), residues: 1486 helix: 1.83 (0.20), residues: 667 sheet: -1.77 (0.41), residues: 164 loop : -2.36 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 229 TYR 0.026 0.002 TYR 3 318 PHE 0.012 0.002 PHE 3 195 TRP 0.011 0.002 TRP 3 303 HIS 0.004 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (10755) covalent geometry : angle 0.61458 / 0.31 (14711) SS BOND : bond 0.00228 / 0.15 ( 18) SS BOND : angle 0.63589 / 0.33 ( 36) hydrogen bonds : bond 0.04028 / 2.69 ( 541) hydrogen bonds : angle 4.10387 / 2.81 ( 1581) link_NAG-ASN : bond 0.00080 / 0.04 ( 2) link_NAG-ASN : angle 0.90743 / 0.38 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 93 time to evaluate : 0.331 Fit side-chains REVERT: 2 43 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7573 (tttt) REVERT: 2 100 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7532 (mp0) REVERT: 2 227 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: 2 269 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7832 (m-80) REVERT: 2 365 HIS cc_start: 0.5165 (OUTLIER) cc_final: 0.4402 (m170) REVERT: 2 373 GLU cc_start: 0.8091 (tp30) cc_final: 0.7803 (tt0) REVERT: 2 375 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: 2 414 ASN cc_start: 0.7940 (t0) cc_final: 0.7543 (t0) REVERT: 2 417 ARG cc_start: 0.8186 (ttp-170) cc_final: 0.7878 (ttm170) REVERT: 2 427 LYS cc_start: 0.8050 (ttmt) cc_final: 0.7775 (ttpt) REVERT: 2 445 ARG cc_start: 0.7845 (mpp-170) cc_final: 0.7552 (mpp-170) REVERT: 3 72 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7703 (ttt) REVERT: 3 228 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6316 (mp0) REVERT: 3 232 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6255 (mp10) REVERT: 3 334 ASP cc_start: 0.7603 (m-30) cc_final: 0.7347 (m-30) REVERT: 3 434 TYR cc_start: 0.8646 (m-80) cc_final: 0.7996 (m-80) REVERT: 3 493 ASP cc_start: 0.7870 (t70) cc_final: 0.7376 (t0) outliers start: 28 outliers final: 13 residues processed: 115 average time/residue: 0.3580 time to fit residues: 45.5376 Evaluate side-chains 111 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 43 LYS Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 134 THR Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 259 GLN Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 41 LEU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 98 THR Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 228 GLU Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 138 optimal weight: 20.0000 chunk 119 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 68 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 115 optimal weight: 0.0870 chunk 107 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 42 GLN 2 56 HIS 2 339 ASN 2 439 ASN 3 473 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.229333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.138257 restraints weight = 11123.932| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.67 r_work: 0.3364 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10775 Z= 0.160 Angle : 0.573 11.336 14753 Z= 0.288 Chirality : 0.042 0.176 1725 Planarity : 0.004 0.039 1930 Dihedral : 4.463 57.754 1601 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.70 % Allowed : 17.41 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.22), residues: 1486 helix: 1.93 (0.20), residues: 667 sheet: -1.68 (0.42), residues: 164 loop : -2.30 (0.22), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 229 TYR 0.026 0.002 TYR 3 318 PHE 0.012 0.001 PHE 3 195 TRP 0.009 0.001 TRP 2 349 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (10755) covalent geometry : angle 0.57319 / 0.29 (14711) SS BOND : bond 0.00205 / 0.12 ( 18) SS BOND : angle 0.57938 / 0.30 ( 36) hydrogen bonds : bond 0.03703 / 2.47 ( 541) hydrogen bonds : angle 3.98469 / 2.73 ( 1581) link_NAG-ASN : bond 0.00059 / 0.03 ( 2) link_NAG-ASN : angle 0.94827 / 0.42 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.251 Fit side-chains REVERT: 2 43 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7596 (tttt) REVERT: 2 227 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: 2 269 PHE cc_start: 0.8517 (OUTLIER) cc_final: 0.7735 (m-80) REVERT: 2 365 HIS cc_start: 0.5094 (OUTLIER) cc_final: 0.4334 (m170) REVERT: 2 373 GLU cc_start: 0.8086 (tp30) cc_final: 0.7851 (tt0) REVERT: 2 375 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.6315 (tm-30) REVERT: 2 414 ASN cc_start: 0.7879 (t0) cc_final: 0.7481 (t0) REVERT: 2 417 ARG cc_start: 0.8172 (ttp-170) cc_final: 0.7862 (ttm170) REVERT: 2 427 LYS cc_start: 0.8021 (ttmt) cc_final: 0.7740 (ttpt) REVERT: 2 445 ARG cc_start: 0.7816 (mpp-170) cc_final: 0.7536 (mpp-170) REVERT: 3 72 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7614 (ttt) REVERT: 3 203 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7601 (mt-10) REVERT: 3 228 GLU cc_start: 0.7240 (OUTLIER) cc_final: 0.6267 (mp0) REVERT: 3 232 GLN cc_start: 0.7076 (OUTLIER) cc_final: 0.6220 (mp10) REVERT: 3 233 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7447 (mm-30) REVERT: 3 263 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6445 (mt) REVERT: 3 334 ASP cc_start: 0.7552 (m-30) cc_final: 0.7299 (m-30) REVERT: 3 434 TYR cc_start: 0.8622 (m-80) cc_final: 0.7976 (m-80) REVERT: 3 493 ASP cc_start: 0.7803 (t70) cc_final: 0.7315 (t0) outliers start: 25 outliers final: 12 residues processed: 113 average time/residue: 0.3615 time to fit residues: 45.0983 Evaluate side-chains 117 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 43 LYS Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 134 THR Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 41 LEU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 98 THR Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 228 GLU Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 141 optimal weight: 40.0000 chunk 90 optimal weight: 0.5980 chunk 45 optimal weight: 0.0070 chunk 124 optimal weight: 7.9990 chunk 134 optimal weight: 30.0000 chunk 0 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 144 optimal weight: 0.3980 chunk 120 optimal weight: 0.7980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 42 GLN 2 56 HIS 2 339 ASN ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.230305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147663 restraints weight = 11061.834| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.73 r_work: 0.3369 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10775 Z= 0.129 Angle : 0.547 11.168 14753 Z= 0.275 Chirality : 0.042 0.168 1725 Planarity : 0.003 0.039 1930 Dihedral : 4.294 56.127 1601 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.49 % Allowed : 17.73 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.22), residues: 1486 helix: 2.03 (0.20), residues: 668 sheet: -1.66 (0.42), residues: 165 loop : -2.21 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 229 TYR 0.025 0.001 TYR 3 318 PHE 0.011 0.001 PHE 3 195 TRP 0.009 0.001 TRP 2 349 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (10755) covalent geometry : angle 0.54675 / 0.27 (14711) SS BOND : bond 0.00170 / 0.10 ( 18) SS BOND : angle 0.51699 / 0.26 ( 36) hydrogen bonds : bond 0.03451 / 2.30 ( 541) hydrogen bonds : angle 3.84857 / 2.63 ( 1581) link_NAG-ASN : bond 0.00019 / 0.01 ( 2) link_NAG-ASN : angle 0.92411 / 0.39 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2972 Ramachandran restraints generated. 1486 Oldfield, 0 Emsley, 1486 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.310 Fit side-chains REVERT: 2 43 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7626 (tttt) REVERT: 2 227 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6398 (mp0) REVERT: 2 269 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: 2 365 HIS cc_start: 0.5096 (OUTLIER) cc_final: 0.4296 (m170) REVERT: 2 373 GLU cc_start: 0.8108 (tp30) cc_final: 0.7873 (tt0) REVERT: 2 375 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.6313 (tm-30) REVERT: 2 414 ASN cc_start: 0.7893 (t0) cc_final: 0.7508 (t0) REVERT: 2 417 ARG cc_start: 0.8215 (ttp-170) cc_final: 0.7879 (ttm170) REVERT: 2 427 LYS cc_start: 0.8033 (ttmt) cc_final: 0.7666 (ttpt) REVERT: 2 445 ARG cc_start: 0.7913 (mpp-170) cc_final: 0.7630 (mpp-170) REVERT: 3 72 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7609 (ttt) REVERT: 3 232 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.6319 (tm-30) REVERT: 3 233 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7570 (mm-30) REVERT: 3 263 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6488 (mt) REVERT: 3 334 ASP cc_start: 0.7573 (m-30) cc_final: 0.7310 (m-30) REVERT: 3 385 GLU cc_start: 0.7505 (tp30) cc_final: 0.7067 (mt-10) REVERT: 3 434 TYR cc_start: 0.8621 (m-80) cc_final: 0.7983 (m-80) REVERT: 3 493 ASP cc_start: 0.7751 (t70) cc_final: 0.7322 (t0) outliers start: 23 outliers final: 10 residues processed: 112 average time/residue: 0.4009 time to fit residues: 49.1516 Evaluate side-chains 110 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 43 LYS Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 226 LEU Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 269 PHE Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 375 GLU Chi-restraints excluded: chain 3 residue 41 LEU Chi-restraints excluded: chain 3 residue 69 LEU Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 98 THR Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 49 optimal weight: 30.0000 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 67 optimal weight: 10.0000 chunk 111 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 8 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 42 GLN 2 56 HIS 2 339 ASN ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.228348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.143543 restraints weight = 11065.358| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.38 r_work: 0.3318 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10775 Z= 0.149 Angle : 0.558 10.944 14753 Z= 0.280 Chirality : 0.042 0.172 1725 Planarity : 0.004 0.039 1930 Dihedral : 4.318 57.285 1601 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.38 % Allowed : 17.84 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.22), residues: 1486 helix: 2.08 (0.20), residues: 667 sheet: -1.61 (0.42), residues: 165 loop : -2.21 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 229 TYR 0.026 0.001 TYR 3 318 PHE 0.012 0.001 PHE 3 195 TRP 0.008 0.001 TRP 2 349 HIS 0.003 0.001 HIS 3 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (10755) covalent geometry : angle 0.55814 / 0.28 (14711) SS BOND : bond 0.00186 / 0.11 ( 18) SS BOND : angle 0.53354 / 0.27 ( 36) hydrogen bonds : bond 0.03573 / 2.37 ( 541) hydrogen bonds : angle 3.84816 / 2.64 ( 1581) link_NAG-ASN : bond 0.00063 / 0.03 ( 2) link_NAG-ASN : angle 0.93892 / 0.40 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3147.60 seconds wall clock time: 54 minutes 11.28 seconds (3251.28 seconds total)