Starting phenix.real_space_refine on Sat Aug 23 07:59:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcz_36170/08_2025/8jcz_36170.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcz_36170/08_2025/8jcz_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_36170/08_2025/8jcz_36170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcz_36170/08_2025/8jcz_36170.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jcz_36170/08_2025/8jcz_36170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcz_36170/08_2025/8jcz_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-2.0-5787/lib/python3.9/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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.48, per 1000 atoms: 0.24 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: 0.87 Conformation dependent library (CDL) restraints added in 527.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.35 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: 1.70 Time building geometry restraints manager: 1.18 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 - 35.86: 6329 35.86 - 71.72: 107 71.72 - 107.57: 12 107.57 - 143.43: 4 143.43 - 179.29: 2 Dihedral angle restraints: 6454 sinusoidal: 2101 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 6451 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: 4.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.760 Find NCS groups from input model: 0.080 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:6.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 14.971 179.291 3582 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 aren 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 covalent geometry : bond 0.00334 (10755) covalent geometry : angle 0.56676 (14711) SS BOND : bond 0.00128 ( 18) SS BOND : angle 0.65952 ( 36) hydrogen bonds : bond 0.13733 ( 541) hydrogen bonds : angle 5.68541 ( 1581) link_NAG-ASN : bond 0.00180 ( 2) link_NAG-ASN : angle 0.61144 ( 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 : 0.294 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 96 average time/residue: 0.4143 time to fit residues: 44.0954 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 : 0.251 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 3 386 GLN 3 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.236276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.155570 restraints weight = 11296.202| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.99 r_work: 0.3423 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.0942 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 : 0.562 10.876 14753 Z= 0.278 Chirality : 0.042 0.197 1725 Planarity : 0.004 0.036 1930 Dihedral : 4.500 48.439 1686 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.30 % Allowed : 6.49 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.22), residues: 1486 helix: 2.23 (0.20), residues: 656 sheet: -0.73 (0.48), residues: 141 loop : -1.95 (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 0.018 0.002 PHE 3 195 TRP 0.008 0.001 TRP 2 297 HIS 0.002 0.001 HIS 3 94 Details of bonding type rmsd covalent geometry : bond 0.00378 (10755) covalent geometry : angle 0.56102 (14711) SS BOND : bond 0.00239 ( 18) SS BOND : angle 0.67925 ( 36) hydrogen bonds : bond 0.03893 ( 541) hydrogen bonds : angle 4.27578 ( 1581) link_NAG-ASN : bond 0.00048 ( 2) link_NAG-ASN : angle 0.99280 ( 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 : 0.434 Fit side-chains REVERT: 2 190 PHE cc_start: 0.8533 (m-10) cc_final: 0.8329 (m-10) REVERT: 2 227 GLU cc_start: 0.6426 (mm-30) cc_final: 0.5981 (mp0) REVERT: 2 373 GLU cc_start: 0.7694 (tp30) cc_final: 0.7394 (tt0) REVERT: 2 410 MET cc_start: 0.6051 (tpt) cc_final: 0.5824 (tpt) REVERT: 2 427 LYS cc_start: 0.7698 (ttmt) cc_final: 0.7431 (ttpt) REVERT: 3 101 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7823 (mtp85) REVERT: 3 199 LYS cc_start: 0.8154 (mtpp) cc_final: 0.7269 (mptp) REVERT: 3 201 MET cc_start: 0.7780 (ptt) cc_final: 0.7525 (ptt) REVERT: 3 334 ASP cc_start: 0.7815 (m-30) cc_final: 0.7581 (m-30) REVERT: 3 434 TYR cc_start: 0.8567 (m-80) cc_final: 0.7585 (m-80) REVERT: 3 493 ASP cc_start: 0.7645 (t0) cc_final: 0.7166 (OUTLIER) outliers start: 12 outliers final: 4 residues processed: 111 average time/residue: 0.4640 time to fit residues: 56.6941 Evaluate side-chains 95 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 92 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 259 GLN 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: 5.9990 chunk 6 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 58 optimal weight: 20.0000 chunk 63 optimal weight: 7.9990 chunk 78 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 110 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 56 HIS 2 374 GLN 3 345 ASN 3 386 GLN 3 472 GLN 3 473 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.228980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.141266 restraints weight = 11154.207| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.84 r_work: 0.3258 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.080 10775 Z= 0.345 Angle : 0.699 9.500 14753 Z= 0.355 Chirality : 0.048 0.197 1725 Planarity : 0.005 0.054 1930 Dihedral : 4.981 50.976 1685 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.05 % Allowed : 10.05 % Favored : 87.89 % 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 aren not related in a simple way. whole: -0.42 (0.22), residues: 1486 helix: 1.78 (0.20), residues: 666 sheet: -1.48 (0.45), residues: 137 loop : -2.24 (0.21), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 2 229 TYR 0.020 0.002 TYR 3 478 PHE 0.016 0.003 PHE 3 440 TRP 0.018 0.003 TRP 3 303 HIS 0.006 0.002 HIS 3 485 Details of bonding type rmsd covalent geometry : bond 0.00831 (10755) covalent geometry : angle 0.69853 (14711) SS BOND : bond 0.00361 ( 18) SS BOND : angle 0.93015 ( 36) hydrogen bonds : bond 0.04855 ( 541) hydrogen bonds : angle 4.44504 ( 1581) link_NAG-ASN : bond 0.00197 ( 2) link_NAG-ASN : angle 1.19322 ( 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 124 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.340 Fit side-chains REVERT: 2 100 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7701 (mp0) REVERT: 2 373 GLU cc_start: 0.8083 (tp30) cc_final: 0.7684 (tt0) REVERT: 2 375 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.6707 (tm-30) REVERT: 2 414 ASN cc_start: 0.7681 (t0) cc_final: 0.7194 (t0) REVERT: 2 427 LYS cc_start: 0.8124 (ttmt) cc_final: 0.7806 (ttpt) REVERT: 3 227 ILE cc_start: 0.7917 (OUTLIER) cc_final: 0.7495 (tp) REVERT: 3 283 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: 3 334 ASP cc_start: 0.7693 (m-30) cc_final: 0.7443 (m-30) REVERT: 3 493 ASP cc_start: 0.7923 (t70) cc_final: 0.7377 (t0) outliers start: 19 outliers final: 5 residues processed: 118 average time/residue: 0.5142 time to fit residues: 66.2031 Evaluate side-chains 96 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain 3 residue 283 GLU Chi-restraints excluded: chain 3 residue 391 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 133 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 113 optimal weight: 0.0970 chunk 112 optimal weight: 4.9990 chunk 49 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 19 optimal weight: 0.0870 chunk 122 optimal weight: 0.2980 chunk 149 optimal weight: 20.0000 overall best weight: 0.8158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4540 r_free = 0.4540 target = 0.230759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.147296 restraints weight = 11217.653| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 4.17 r_work: 0.3346 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10775 Z= 0.175 Angle : 0.561 7.586 14753 Z= 0.284 Chirality : 0.042 0.160 1725 Planarity : 0.004 0.041 1930 Dihedral : 4.528 52.808 1685 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.73 % Allowed : 13.41 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.22), residues: 1486 helix: 1.87 (0.20), residues: 664 sheet: -1.44 (0.44), residues: 147 loop : -2.27 (0.21), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 3 235 TYR 0.011 0.001 TYR 2 180 PHE 0.014 0.002 PHE 3 195 TRP 0.010 0.001 TRP 3 297 HIS 0.003 0.001 HIS 3 94 Details of bonding type rmsd covalent geometry : bond 0.00418 (10755) covalent geometry : angle 0.56091 (14711) SS BOND : bond 0.00223 ( 18) SS BOND : angle 0.62651 ( 36) hydrogen bonds : bond 0.03904 ( 541) hydrogen bonds : angle 4.19091 ( 1581) link_NAG-ASN : bond 0.00046 ( 2) link_NAG-ASN : angle 1.19331 ( 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 114 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.345 Fit side-chains REVERT: 2 43 LYS cc_start: 0.8016 (ttpp) cc_final: 0.7649 (tttt) REVERT: 2 227 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6385 (mp0) REVERT: 2 375 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6485 (tm-30) REVERT: 2 410 MET cc_start: 0.6544 (tpt) cc_final: 0.6061 (tpt) REVERT: 2 414 ASN cc_start: 0.7738 (t0) cc_final: 0.7255 (t0) REVERT: 2 427 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7798 (ttpt) REVERT: 3 72 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7662 (ttt) REVERT: 3 228 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: 3 334 ASP cc_start: 0.7717 (m-30) cc_final: 0.7509 (m-30) REVERT: 3 434 TYR cc_start: 0.8641 (m-80) cc_final: 0.7650 (m-80) REVERT: 3 493 ASP cc_start: 0.7878 (t70) cc_final: 0.7459 (t0) outliers start: 16 outliers final: 4 residues processed: 111 average time/residue: 0.5027 time to fit residues: 60.9638 Evaluate side-chains 97 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 227 GLU 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 228 GLU Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 494 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 22 optimal weight: 2.9990 chunk 136 optimal weight: 30.0000 chunk 71 optimal weight: 40.0000 chunk 48 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 73 optimal weight: 30.0000 chunk 39 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4486 r_free = 0.4486 target = 0.224917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.137997 restraints weight = 11057.901| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.83 r_work: 0.3311 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 10775 Z= 0.268 Angle : 0.635 8.100 14753 Z= 0.323 Chirality : 0.046 0.206 1725 Planarity : 0.004 0.044 1930 Dihedral : 4.743 55.076 1685 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.46 % Allowed : 13.51 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.22), residues: 1486 helix: 1.73 (0.20), residues: 668 sheet: -1.72 (0.43), residues: 145 loop : -2.34 (0.21), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 235 TYR 0.017 0.002 TYR 2 473 PHE 0.014 0.002 PHE 2 348 TRP 0.014 0.002 TRP 3 303 HIS 0.004 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00649 (10755) covalent geometry : angle 0.63427 (14711) SS BOND : bond 0.00283 ( 18) SS BOND : angle 0.73756 ( 36) hydrogen bonds : bond 0.04369 ( 541) hydrogen bonds : angle 4.27212 ( 1581) link_NAG-ASN : bond 0.00172 ( 2) link_NAG-ASN : angle 1.08926 ( 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 126 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: 2 29 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6382 (mt-10) REVERT: 2 227 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: 2 285 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7656 (mt) REVERT: 2 375 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.6543 (tm-30) REVERT: 2 410 MET cc_start: 0.6525 (tpt) cc_final: 0.5850 (tpt) REVERT: 2 414 ASN cc_start: 0.7788 (t0) cc_final: 0.7309 (t0) REVERT: 2 427 LYS cc_start: 0.8066 (ttmt) cc_final: 0.7782 (ttpt) REVERT: 2 439 ASN cc_start: 0.7036 (m110) cc_final: 0.6729 (p0) REVERT: 3 283 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8079 (mt-10) REVERT: 3 334 ASP cc_start: 0.7633 (m-30) cc_final: 0.7377 (m-30) REVERT: 3 434 TYR cc_start: 0.8666 (m-80) cc_final: 0.7697 (m-80) REVERT: 3 493 ASP cc_start: 0.7894 (t70) cc_final: 0.7377 (t0) outliers start: 32 outliers final: 9 residues processed: 117 average time/residue: 0.4470 time to fit residues: 57.4333 Evaluate side-chains 103 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 100 GLU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 259 GLN 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 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 283 GLU Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 494 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 47 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 54 optimal weight: 30.0000 chunk 37 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 56 HIS 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.228755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.143807 restraints weight = 11093.241| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.14 r_work: 0.3319 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10775 Z= 0.154 Angle : 0.537 6.316 14753 Z= 0.275 Chirality : 0.042 0.156 1725 Planarity : 0.004 0.037 1930 Dihedral : 4.411 56.577 1685 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.70 % Allowed : 14.49 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.22), residues: 1486 helix: 1.87 (0.20), residues: 669 sheet: -1.45 (0.43), residues: 156 loop : -2.29 (0.22), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 235 TYR 0.011 0.001 TYR 3 256 PHE 0.014 0.001 PHE 3 195 TRP 0.010 0.001 TRP 2 487 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00363 (10755) covalent geometry : angle 0.53686 (14711) SS BOND : bond 0.00203 ( 18) SS BOND : angle 0.57009 ( 36) hydrogen bonds : bond 0.03729 ( 541) hydrogen bonds : angle 4.05984 ( 1581) link_NAG-ASN : bond 0.00055 ( 2) link_NAG-ASN : angle 1.07633 ( 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 121 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.331 Fit side-chains revert: symmetry clash REVERT: 2 43 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7749 (tttt) REVERT: 2 285 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7758 (mt) REVERT: 2 375 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: 2 410 MET cc_start: 0.6518 (tpt) cc_final: 0.5152 (tpt) REVERT: 2 414 ASN cc_start: 0.7877 (t0) cc_final: 0.7451 (t0) REVERT: 2 427 LYS cc_start: 0.8081 (ttmt) cc_final: 0.7817 (ttpt) REVERT: 2 439 ASN cc_start: 0.7040 (m110) cc_final: 0.6741 (p0) REVERT: 2 445 ARG cc_start: 0.7920 (mpp-170) cc_final: 0.7714 (mpp-170) REVERT: 3 72 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7666 (ttt) REVERT: 3 263 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6356 (mt) REVERT: 3 334 ASP cc_start: 0.7708 (m-30) cc_final: 0.7478 (m-30) REVERT: 3 434 TYR cc_start: 0.8638 (m-80) cc_final: 0.7741 (m-80) REVERT: 3 493 ASP cc_start: 0.7888 (t70) cc_final: 0.7465 (t0) outliers start: 25 outliers final: 12 residues processed: 113 average time/residue: 0.4771 time to fit residues: 59.4553 Evaluate side-chains 108 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 100 GLU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 259 GLN 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 72 MET Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 243 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 77 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 82 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 114 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 56 HIS 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 = 0.4538 r_free = 0.4538 target = 0.230213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.144188 restraints weight = 11213.703| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.83 r_work: 0.3345 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10775 Z= 0.159 Angle : 0.549 7.803 14753 Z= 0.278 Chirality : 0.042 0.154 1725 Planarity : 0.004 0.049 1930 Dihedral : 4.299 56.703 1685 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.14 % Allowed : 14.70 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.22), residues: 1486 helix: 1.95 (0.20), residues: 669 sheet: -1.60 (0.42), residues: 163 loop : -2.24 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG 3 235 TYR 0.025 0.001 TYR 3 318 PHE 0.012 0.001 PHE 3 275 TRP 0.008 0.001 TRP 2 487 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00379 (10755) covalent geometry : angle 0.54877 (14711) SS BOND : bond 0.00204 ( 18) SS BOND : angle 0.55328 ( 36) hydrogen bonds : bond 0.03678 ( 541) hydrogen bonds : angle 3.97062 ( 1581) link_NAG-ASN : bond 0.00090 ( 2) link_NAG-ASN : angle 1.05624 ( 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 125 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: 2 43 LYS cc_start: 0.7980 (OUTLIER) cc_final: 0.7600 (tttt) REVERT: 2 227 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6493 (mp0) REVERT: 2 285 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7717 (mt) REVERT: 2 375 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.6442 (tm-30) REVERT: 2 410 MET cc_start: 0.6633 (tpt) cc_final: 0.5259 (tpt) REVERT: 2 414 ASN cc_start: 0.7789 (t0) cc_final: 0.7330 (t0) REVERT: 2 427 LYS cc_start: 0.8031 (ttmt) cc_final: 0.7759 (ttpt) REVERT: 2 439 ASN cc_start: 0.7012 (m110) cc_final: 0.6739 (p0) REVERT: 2 445 ARG cc_start: 0.7924 (mpp-170) cc_final: 0.7671 (mpp-170) REVERT: 3 72 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.7635 (ttt) REVERT: 3 263 LEU cc_start: 0.6663 (OUTLIER) cc_final: 0.6430 (mt) REVERT: 3 334 ASP cc_start: 0.7611 (m-30) cc_final: 0.7339 (m-30) REVERT: 3 434 TYR cc_start: 0.8625 (m-80) cc_final: 0.7679 (m-80) REVERT: 3 493 ASP cc_start: 0.7799 (t70) cc_final: 0.7429 (t70) outliers start: 29 outliers final: 13 residues processed: 117 average time/residue: 0.4183 time to fit residues: 54.0896 Evaluate side-chains 109 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.370 ------------------------------------------------------------------------------- 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 100 GLU 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 285 LEU Chi-restraints excluded: chain 2 residue 317 ILE 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 227 ILE Chi-restraints excluded: chain 3 residue 243 THR Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 481 LEU 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: 0.3980 chunk 88 optimal weight: 0.7980 chunk 42 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 0.0070 chunk 93 optimal weight: 0.9990 chunk 50 optimal weight: 0.0670 chunk 118 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 56 HIS ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 473 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.231648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.146321 restraints weight = 11093.193| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.52 r_work: 0.3376 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10775 Z= 0.113 Angle : 0.527 12.887 14753 Z= 0.264 Chirality : 0.041 0.136 1725 Planarity : 0.003 0.038 1930 Dihedral : 4.177 55.723 1685 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.27 % Allowed : 16.43 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.22), residues: 1486 helix: 2.07 (0.20), residues: 670 sheet: -1.51 (0.43), residues: 165 loop : -2.17 (0.22), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 3 235 TYR 0.024 0.001 TYR 3 318 PHE 0.013 0.001 PHE 3 275 TRP 0.010 0.001 TRP 2 487 HIS 0.002 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00260 (10755) covalent geometry : angle 0.52700 (14711) SS BOND : bond 0.00171 ( 18) SS BOND : angle 0.47788 ( 36) hydrogen bonds : bond 0.03379 ( 541) hydrogen bonds : angle 3.84051 ( 1581) link_NAG-ASN : bond 0.00076 ( 2) link_NAG-ASN : angle 0.96080 ( 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 117 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: 2 43 LYS cc_start: 0.7925 (ttpp) cc_final: 0.7595 (tttt) REVERT: 2 227 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: 2 375 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.6347 (tm-30) REVERT: 2 410 MET cc_start: 0.6672 (tpt) cc_final: 0.5701 (tpt) REVERT: 2 414 ASN cc_start: 0.7745 (t0) cc_final: 0.7316 (t0) REVERT: 2 417 ARG cc_start: 0.8163 (ttp-170) cc_final: 0.7770 (ttm170) REVERT: 2 427 LYS cc_start: 0.8028 (ttmt) cc_final: 0.7728 (ttpt) REVERT: 2 439 ASN cc_start: 0.7053 (m110) cc_final: 0.6774 (p0) REVERT: 2 445 ARG cc_start: 0.7939 (mpp-170) cc_final: 0.7674 (mpp-170) REVERT: 3 72 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7576 (ttt) REVERT: 3 199 LYS cc_start: 0.8268 (mtpp) cc_final: 0.7342 (mptt) REVERT: 3 219 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: 3 334 ASP cc_start: 0.7587 (m-30) cc_final: 0.7297 (m-30) REVERT: 3 434 TYR cc_start: 0.8591 (m-80) cc_final: 0.7633 (m-80) REVERT: 3 493 ASP cc_start: 0.7680 (t70) cc_final: 0.7325 (t70) outliers start: 21 outliers final: 10 residues processed: 111 average time/residue: 0.4820 time to fit residues: 58.5563 Evaluate side-chains 109 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 100 GLU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 227 GLU 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 191 VAL Chi-restraints excluded: chain 3 residue 219 GLU Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 243 THR Chi-restraints excluded: chain 3 residue 481 LEU 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: 0.6980 chunk 72 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 chunk 115 optimal weight: 0.3980 chunk 107 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4540 r_free = 0.4540 target = 0.230351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.145515 restraints weight = 11133.635| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.69 r_work: 0.3293 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10775 Z= 0.155 Angle : 0.559 11.195 14753 Z= 0.279 Chirality : 0.042 0.150 1725 Planarity : 0.004 0.038 1930 Dihedral : 4.244 56.303 1685 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.38 % Allowed : 16.65 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.22), residues: 1486 helix: 2.07 (0.20), residues: 667 sheet: -1.55 (0.42), residues: 165 loop : -2.20 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 3 235 TYR 0.026 0.002 TYR 3 318 PHE 0.014 0.001 PHE 3 275 TRP 0.008 0.001 TRP 3 303 HIS 0.002 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00371 (10755) covalent geometry : angle 0.55896 (14711) SS BOND : bond 0.00187 ( 18) SS BOND : angle 0.51225 ( 36) hydrogen bonds : bond 0.03612 ( 541) hydrogen bonds : angle 3.86259 ( 1581) link_NAG-ASN : bond 0.00032 ( 2) link_NAG-ASN : angle 0.95403 ( 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 114 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.407 Fit side-chains revert: symmetry clash REVERT: 2 43 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7604 (tttt) REVERT: 2 227 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: 2 375 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.6473 (tm-30) REVERT: 2 410 MET cc_start: 0.6657 (tpt) cc_final: 0.5507 (tpt) REVERT: 2 414 ASN cc_start: 0.7839 (t0) cc_final: 0.7377 (t0) REVERT: 2 427 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7773 (ttpt) REVERT: 2 439 ASN cc_start: 0.7107 (m110) cc_final: 0.6754 (p0) REVERT: 2 445 ARG cc_start: 0.7969 (mpp-170) cc_final: 0.7692 (mpp-170) REVERT: 3 72 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7694 (ttt) REVERT: 3 219 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7148 (pm20) REVERT: 3 334 ASP cc_start: 0.7696 (m-30) cc_final: 0.7399 (m-30) REVERT: 3 434 TYR cc_start: 0.8641 (m-80) cc_final: 0.7610 (m-80) REVERT: 3 493 ASP cc_start: 0.7818 (t70) cc_final: 0.7441 (t70) outliers start: 22 outliers final: 11 residues processed: 108 average time/residue: 0.4976 time to fit residues: 59.0143 Evaluate side-chains 108 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 100 GLU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 317 ILE 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 219 GLU Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 481 LEU 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: 10.0000 chunk 3 optimal weight: 0.3980 chunk 141 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 134 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 144 optimal weight: 0.0030 chunk 120 optimal weight: 0.6980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4545 r_free = 0.4545 target = 0.230927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.145629 restraints weight = 11083.445| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.72 r_work: 0.3365 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10775 Z= 0.138 Angle : 0.551 11.071 14753 Z= 0.275 Chirality : 0.042 0.148 1725 Planarity : 0.003 0.037 1930 Dihedral : 4.225 56.293 1685 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.38 % Allowed : 16.86 % Favored : 80.76 % 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 aren not related in a simple way. whole: -0.14 (0.22), residues: 1486 helix: 2.10 (0.20), residues: 669 sheet: -1.54 (0.42), residues: 165 loop : -2.16 (0.22), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 3 235 TYR 0.026 0.001 TYR 3 318 PHE 0.012 0.001 PHE 3 195 TRP 0.007 0.001 TRP 2 349 HIS 0.002 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00327 (10755) covalent geometry : angle 0.55062 (14711) SS BOND : bond 0.00177 ( 18) SS BOND : angle 0.48841 ( 36) hydrogen bonds : bond 0.03493 ( 541) hydrogen bonds : angle 3.81405 ( 1581) link_NAG-ASN : bond 0.00013 ( 2) link_NAG-ASN : angle 0.95016 ( 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 117 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: 2 43 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7589 (tttt) REVERT: 2 227 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: 2 339 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7912 (t0) REVERT: 2 375 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.6350 (tm-30) REVERT: 2 410 MET cc_start: 0.6699 (tpt) cc_final: 0.5627 (tpt) REVERT: 2 414 ASN cc_start: 0.7752 (t0) cc_final: 0.7306 (t0) REVERT: 2 427 LYS cc_start: 0.8001 (ttmt) cc_final: 0.7704 (ttpt) REVERT: 2 439 ASN cc_start: 0.7074 (m110) cc_final: 0.6784 (p0) REVERT: 2 445 ARG cc_start: 0.7932 (mpp-170) cc_final: 0.7678 (mpp-170) REVERT: 3 72 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7613 (ttt) REVERT: 3 203 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7243 (mm-30) REVERT: 3 219 GLU cc_start: 0.7301 (OUTLIER) cc_final: 0.7069 (pm20) REVERT: 3 263 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6332 (mt) REVERT: 3 334 ASP cc_start: 0.7572 (m-30) cc_final: 0.7284 (m-30) REVERT: 3 434 TYR cc_start: 0.8598 (m-80) cc_final: 0.7561 (m-80) REVERT: 3 493 ASP cc_start: 0.7724 (t70) cc_final: 0.7362 (t70) outliers start: 22 outliers final: 11 residues processed: 111 average time/residue: 0.4621 time to fit residues: 56.4047 Evaluate side-chains 112 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 100 GLU Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 227 GLU Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 2 residue 339 ASN 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 219 GLU Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 481 LEU 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: 10.0000 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 51 optimal weight: 20.0000 chunk 8 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 56 HIS 2 339 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.227991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.152534 restraints weight = 11061.118| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.45 r_work: 0.3346 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2767 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= 0.181 Angle : 0.585 10.808 14753 Z= 0.293 Chirality : 0.043 0.158 1725 Planarity : 0.004 0.038 1930 Dihedral : 4.312 55.889 1685 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.70 % Allowed : 16.65 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.22), residues: 1486 helix: 2.06 (0.20), residues: 667 sheet: -1.61 (0.42), residues: 165 loop : -2.20 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG 3 235 TYR 0.027 0.002 TYR 3 318 PHE 0.013 0.002 PHE 3 275 TRP 0.009 0.001 TRP 2 337 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00436 (10755) covalent geometry : angle 0.58437 (14711) SS BOND : bond 0.00208 ( 18) SS BOND : angle 0.56177 ( 36) hydrogen bonds : bond 0.03707 ( 541) hydrogen bonds : angle 3.86640 ( 1581) link_NAG-ASN : bond 0.00042 ( 2) link_NAG-ASN : angle 0.94246 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3758.00 seconds wall clock time: 64 minutes 39.28 seconds (3879.28 seconds total)