Starting phenix.real_space_refine on Mon Jul 28 21:46:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcz_36170/07_2025/8jcz_36170.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcz_36170/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jcz_36170/07_2025/8jcz_36170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcz_36170/07_2025/8jcz_36170.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcz_36170/07_2025/8jcz_36170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcz_36170/07_2025/8jcz_36170.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 8, 'TRP:plan': 3, 'ASP:plan': 7, 'PHE:plan': 13, 'GLU:plan': 16, 'ARG:plan': 19} 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: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 10, 'ASN:plan1': 10, 'TRP:plan': 4, 'ASP:plan': 9, 'PHE:plan': 13, 'GLU:plan': 11, 'ARG:plan': 15} 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: 7.31, per 1000 atoms: 0.69 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: 2.56 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.31 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: 3.15 Time building geometry restraints manager: 3.08 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: 4.710 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: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.460 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.990 ------------------------------------------------------------------------------- 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 : 9.10 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (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 TRP 0.006 0.001 TRP 2 297 HIS 0.004 0.001 HIS 2 77 PHE 0.008 0.001 PHE 3 195 TYR 0.023 0.001 TYR 3 256 ARG 0.004 0.000 ARG 2 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 2) link_NAG-ASN : angle 0.61144 ( 6) hydrogen bonds : bond 0.13733 ( 541) hydrogen bonds : angle 5.68541 ( 1581) SS BOND : bond 0.00128 ( 18) SS BOND : angle 0.65952 ( 36) covalent geometry : bond 0.00334 (10755) covalent geometry : angle 0.56676 (14711) *********************** 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 : 1.510 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 96 average time/residue: 1.0824 time to fit residues: 115.6295 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 : 1.111 ------------------------------------------------------------------------------- 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 126 optimal weight: 10.0000 chunk 113 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 45 optimal weight: 0.0020 chunk 71 optimal weight: 7.9990 chunk 87 optimal weight: 0.0030 chunk 136 optimal weight: 5.9990 overall best weight: 1.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4559 r_free = 0.4559 target = 0.233082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.153195 restraints weight = 11055.242| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 3.91 r_work: 0.3421 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 10775 Z= 0.248 Angle : 0.648 12.264 14753 Z= 0.323 Chirality : 0.045 0.197 1725 Planarity : 0.004 0.052 1930 Dihedral : 4.768 51.093 1686 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.30 % Allowed : 8.32 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1486 helix: 2.05 (0.20), residues: 658 sheet: -0.94 (0.48), residues: 135 loop : -2.06 (0.22), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 3 303 HIS 0.004 0.001 HIS 3 94 PHE 0.015 0.002 PHE 3 195 TYR 0.015 0.002 TYR 2 165 ARG 0.006 0.001 ARG 2 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 2) link_NAG-ASN : angle 1.16180 ( 6) hydrogen bonds : bond 0.04322 ( 541) hydrogen bonds : angle 4.39795 ( 1581) SS BOND : bond 0.00304 ( 18) SS BOND : angle 0.85154 ( 36) covalent geometry : bond 0.00587 (10755) covalent geometry : angle 0.64694 (14711) *********************** 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 115 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 1.081 Fit side-chains REVERT: 2 29 GLU cc_start: 0.6378 (mp0) cc_final: 0.6168 (mp0) REVERT: 2 190 PHE cc_start: 0.8546 (m-10) cc_final: 0.8343 (m-10) REVERT: 2 227 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6341 (mp0) REVERT: 2 233 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7485 (pt) REVERT: 2 410 MET cc_start: 0.6389 (tpt) cc_final: 0.6166 (tpt) REVERT: 2 427 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7647 (ttpt) REVERT: 3 201 MET cc_start: 0.7961 (ptt) cc_final: 0.7723 (ptt) REVERT: 3 434 TYR cc_start: 0.8497 (m-80) cc_final: 0.7455 (m-80) REVERT: 3 493 ASP cc_start: 0.7809 (t0) cc_final: 0.7400 (t0) outliers start: 12 outliers final: 4 residues processed: 111 average time/residue: 1.1814 time to fit residues: 144.4649 Evaluate side-chains 95 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 233 ILE Chi-restraints excluded: chain 2 residue 259 GLN Chi-restraints excluded: chain 2 residue 317 ILE Chi-restraints excluded: chain 3 residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 0.0770 chunk 86 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 129 optimal weight: 20.0000 chunk 81 optimal weight: 0.0870 overall best weight: 0.4316 ------------------------------------------------------------------------------- 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 = 0.4576 r_free = 0.4576 target = 0.234903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.169006 restraints weight = 11234.066| |-----------------------------------------------------------------------------| r_work (start): 0.3973 rms_B_bonded: 2.04 r_work: 0.3609 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10775 Z= 0.118 Angle : 0.503 6.871 14753 Z= 0.255 Chirality : 0.041 0.149 1725 Planarity : 0.003 0.035 1930 Dihedral : 4.341 54.562 1685 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.62 % Allowed : 9.41 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1486 helix: 2.15 (0.20), residues: 660 sheet: -1.21 (0.45), residues: 154 loop : -2.08 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 291 HIS 0.003 0.001 HIS 3 485 PHE 0.014 0.001 PHE 2 327 TYR 0.012 0.001 TYR 3 478 ARG 0.005 0.000 ARG 2 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 2) link_NAG-ASN : angle 1.12760 ( 6) hydrogen bonds : bond 0.03643 ( 541) hydrogen bonds : angle 4.10840 ( 1581) SS BOND : bond 0.00179 ( 18) SS BOND : angle 0.51838 ( 36) covalent geometry : bond 0.00266 (10755) covalent geometry : angle 0.50277 (14711) *********************** 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 118 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 1.157 Fit side-chains REVERT: 2 29 GLU cc_start: 0.6251 (mp0) cc_final: 0.5961 (mp0) REVERT: 2 43 LYS cc_start: 0.7426 (ttmm) cc_final: 0.7095 (tttt) REVERT: 2 190 PHE cc_start: 0.8603 (m-10) cc_final: 0.8304 (m-10) REVERT: 2 233 ILE cc_start: 0.7645 (OUTLIER) cc_final: 0.7427 (pt) REVERT: 2 375 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.6689 (tm-30) REVERT: 2 410 MET cc_start: 0.6366 (tpt) cc_final: 0.5821 (tpt) REVERT: 2 414 ASN cc_start: 0.7246 (t0) cc_final: 0.6798 (t0) REVERT: 2 427 LYS cc_start: 0.7900 (ttmt) cc_final: 0.7683 (ttpt) REVERT: 3 199 LYS cc_start: 0.8423 (mtpp) cc_final: 0.7697 (mptt) REVERT: 3 434 TYR cc_start: 0.8511 (m-80) cc_final: 0.7543 (m-80) REVERT: 3 493 ASP cc_start: 0.7691 (t0) cc_final: 0.7405 (t70) outliers start: 15 outliers final: 5 residues processed: 115 average time/residue: 1.0293 time to fit residues: 130.3587 Evaluate side-chains 100 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 1.136 ------------------------------------------------------------------------------- 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 233 ILE 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 481 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 117 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 145 optimal weight: 20.0000 chunk 78 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 0.0870 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN 2 342 ASN 3 472 GLN 3 473 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.232912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.144076 restraints weight = 11128.094| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.03 r_work: 0.3304 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10775 Z= 0.151 Angle : 0.526 7.401 14753 Z= 0.266 Chirality : 0.042 0.160 1725 Planarity : 0.003 0.036 1930 Dihedral : 4.263 54.180 1685 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.84 % Allowed : 11.78 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1486 helix: 2.11 (0.20), residues: 665 sheet: -1.26 (0.46), residues: 146 loop : -2.16 (0.22), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 291 HIS 0.002 0.001 HIS 3 485 PHE 0.013 0.001 PHE 3 195 TYR 0.022 0.001 TYR 3 318 ARG 0.007 0.000 ARG 2 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00058 ( 2) link_NAG-ASN : angle 1.17410 ( 6) hydrogen bonds : bond 0.03647 ( 541) hydrogen bonds : angle 3.99532 ( 1581) SS BOND : bond 0.00205 ( 18) SS BOND : angle 0.57133 ( 36) covalent geometry : bond 0.00358 (10755) covalent geometry : angle 0.52538 (14711) *********************** 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 115 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 1.079 Fit side-chains REVERT: 2 29 GLU cc_start: 0.6412 (mp0) cc_final: 0.6074 (mp0) REVERT: 2 227 GLU cc_start: 0.6527 (OUTLIER) cc_final: 0.6174 (mp0) REVERT: 2 233 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7438 (pt) REVERT: 2 375 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.6685 (tm-30) REVERT: 2 410 MET cc_start: 0.6392 (tpt) cc_final: 0.5608 (tpt) REVERT: 2 414 ASN cc_start: 0.7394 (t0) cc_final: 0.6855 (t0) REVERT: 2 427 LYS cc_start: 0.7996 (ttmt) cc_final: 0.7472 (tttp) REVERT: 3 199 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7429 (mptt) REVERT: 3 227 ILE cc_start: 0.7669 (OUTLIER) cc_final: 0.7176 (tp) REVERT: 3 493 ASP cc_start: 0.7702 (t70) cc_final: 0.7302 (t70) outliers start: 17 outliers final: 7 residues processed: 110 average time/residue: 1.1419 time to fit residues: 138.8239 Evaluate side-chains 104 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE 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 121 optimal weight: 0.0040 chunk 24 optimal weight: 0.8980 chunk 107 optimal weight: 0.2980 chunk 133 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 98 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 chunk 66 optimal weight: 8.9990 chunk 49 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.233259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.150148 restraints weight = 11079.268| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.26 r_work: 0.3374 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1864 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= 0.131 Angle : 0.510 8.275 14753 Z= 0.258 Chirality : 0.041 0.151 1725 Planarity : 0.003 0.036 1930 Dihedral : 4.109 53.091 1685 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.16 % Allowed : 12.54 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.22), residues: 1486 helix: 2.15 (0.20), residues: 664 sheet: -1.23 (0.46), residues: 145 loop : -2.17 (0.22), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 291 HIS 0.001 0.001 HIS 2 438 PHE 0.013 0.001 PHE 2 327 TYR 0.022 0.001 TYR 3 318 ARG 0.005 0.000 ARG 2 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00070 ( 2) link_NAG-ASN : angle 1.13858 ( 6) hydrogen bonds : bond 0.03489 ( 541) hydrogen bonds : angle 3.91901 ( 1581) SS BOND : bond 0.00184 ( 18) SS BOND : angle 0.50192 ( 36) covalent geometry : bond 0.00306 (10755) covalent geometry : angle 0.50948 (14711) *********************** 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 114 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 1.158 Fit side-chains REVERT: 2 29 GLU cc_start: 0.6363 (mp0) cc_final: 0.6063 (mp0) REVERT: 2 43 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7440 (tttt) REVERT: 2 100 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7382 (mp0) REVERT: 2 227 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: 2 233 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7470 (pt) REVERT: 2 375 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.6414 (tm-30) REVERT: 2 410 MET cc_start: 0.6573 (tpt) cc_final: 0.5284 (tpt) REVERT: 2 414 ASN cc_start: 0.7381 (t0) cc_final: 0.6812 (t0) REVERT: 2 427 LYS cc_start: 0.7842 (ttmt) cc_final: 0.7268 (tttp) REVERT: 3 72 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7612 (ttt) REVERT: 3 227 ILE cc_start: 0.8125 (OUTLIER) cc_final: 0.7869 (mm) REVERT: 3 493 ASP cc_start: 0.7604 (t70) cc_final: 0.7208 (t70) outliers start: 20 outliers final: 8 residues processed: 108 average time/residue: 1.0588 time to fit residues: 125.4446 Evaluate side-chains 107 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.039 ------------------------------------------------------------------------------- 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 227 GLU Chi-restraints excluded: chain 2 residue 233 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 6 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 44 optimal weight: 0.0770 chunk 113 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 55 optimal weight: 0.4980 chunk 104 optimal weight: 0.9990 chunk 140 optimal weight: 0.0570 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4573 r_free = 0.4573 target = 0.234558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.154457 restraints weight = 11078.960| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 3.95 r_work: 0.3460 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10775 Z= 0.102 Angle : 0.482 6.959 14753 Z= 0.244 Chirality : 0.040 0.137 1725 Planarity : 0.003 0.037 1930 Dihedral : 3.973 53.773 1685 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.16 % Allowed : 13.19 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.23), residues: 1486 helix: 2.24 (0.20), residues: 668 sheet: -1.21 (0.45), residues: 162 loop : -2.12 (0.22), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 487 HIS 0.001 0.000 HIS 2 87 PHE 0.016 0.001 PHE 2 327 TYR 0.024 0.001 TYR 3 318 ARG 0.009 0.000 ARG 2 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00098 ( 2) link_NAG-ASN : angle 1.12503 ( 6) hydrogen bonds : bond 0.03194 ( 541) hydrogen bonds : angle 3.76179 ( 1581) SS BOND : bond 0.00150 ( 18) SS BOND : angle 0.42468 ( 36) covalent geometry : bond 0.00233 (10755) covalent geometry : angle 0.48138 (14711) *********************** 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 118 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 1.284 Fit side-chains REVERT: 2 29 GLU cc_start: 0.6406 (mp0) cc_final: 0.6089 (mp0) REVERT: 2 43 LYS cc_start: 0.7820 (ttpp) cc_final: 0.7557 (tttt) REVERT: 2 375 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7012 (tt0) REVERT: 2 414 ASN cc_start: 0.7426 (t0) cc_final: 0.7175 (t0) REVERT: 2 427 LYS cc_start: 0.7835 (ttmt) cc_final: 0.7545 (ttpt) REVERT: 3 72 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7485 (ttt) REVERT: 3 434 TYR cc_start: 0.8503 (m-80) cc_final: 0.7471 (m-80) outliers start: 20 outliers final: 7 residues processed: 113 average time/residue: 1.4110 time to fit residues: 176.2062 Evaluate side-chains 102 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL 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 93 VAL Chi-restraints excluded: chain 3 residue 191 VAL Chi-restraints excluded: chain 3 residue 481 LEU 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 98 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 20.0000 chunk 22 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 51 optimal weight: 0.0970 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.232847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.147817 restraints weight = 11259.389| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 3.77 r_work: 0.3339 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10775 Z= 0.134 Angle : 0.528 13.053 14753 Z= 0.263 Chirality : 0.041 0.144 1725 Planarity : 0.003 0.036 1930 Dihedral : 4.014 54.105 1685 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.38 % Allowed : 13.62 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.22), residues: 1486 helix: 2.25 (0.20), residues: 664 sheet: -1.09 (0.46), residues: 156 loop : -2.14 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 3 303 HIS 0.002 0.001 HIS 3 94 PHE 0.012 0.001 PHE 3 275 TYR 0.023 0.001 TYR 3 318 ARG 0.008 0.000 ARG 2 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 2) link_NAG-ASN : angle 1.05385 ( 6) hydrogen bonds : bond 0.03434 ( 541) hydrogen bonds : angle 3.78704 ( 1581) SS BOND : bond 0.00174 ( 18) SS BOND : angle 0.49038 ( 36) covalent geometry : bond 0.00316 (10755) covalent geometry : angle 0.52794 (14711) *********************** 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 120 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 1.048 Fit side-chains REVERT: 2 29 GLU cc_start: 0.6437 (mp0) cc_final: 0.6080 (mp0) REVERT: 2 43 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7494 (tttt) REVERT: 2 100 GLU cc_start: 0.7655 (mt-10) cc_final: 0.7431 (mp0) REVERT: 2 227 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6282 (mp0) REVERT: 2 375 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6418 (tm-30) REVERT: 2 410 MET cc_start: 0.6396 (tpt) cc_final: 0.5778 (tpt) REVERT: 2 414 ASN cc_start: 0.7710 (t0) cc_final: 0.7093 (t0) REVERT: 2 427 LYS cc_start: 0.7921 (ttmt) cc_final: 0.7558 (ttpt) REVERT: 3 72 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7653 (ttt) REVERT: 3 263 LEU cc_start: 0.6366 (OUTLIER) cc_final: 0.6164 (mt) REVERT: 3 283 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: 3 434 TYR cc_start: 0.8607 (m-80) cc_final: 0.7512 (m-80) outliers start: 22 outliers final: 8 residues processed: 114 average time/residue: 1.0072 time to fit residues: 126.2975 Evaluate side-chains 107 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 1.156 ------------------------------------------------------------------------------- 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 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 191 VAL Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 283 GLU 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 37 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 125 optimal weight: 10.0000 chunk 108 optimal weight: 0.4980 chunk 77 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4552 r_free = 0.4552 target = 0.232104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.150701 restraints weight = 11098.220| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 4.13 r_work: 0.3420 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2271 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= 0.151 Angle : 0.548 10.264 14753 Z= 0.273 Chirality : 0.042 0.155 1725 Planarity : 0.003 0.036 1930 Dihedral : 4.088 54.494 1685 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.27 % Allowed : 14.05 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.22), residues: 1486 helix: 2.19 (0.20), residues: 671 sheet: -1.22 (0.45), residues: 156 loop : -2.12 (0.22), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 303 HIS 0.002 0.001 HIS 2 438 PHE 0.012 0.001 PHE 3 195 TYR 0.024 0.001 TYR 3 318 ARG 0.007 0.000 ARG 2 229 Details of bonding type rmsd link_NAG-ASN : bond 0.00018 ( 2) link_NAG-ASN : angle 0.97841 ( 6) hydrogen bonds : bond 0.03557 ( 541) hydrogen bonds : angle 3.81959 ( 1581) SS BOND : bond 0.00189 ( 18) SS BOND : angle 0.49994 ( 36) covalent geometry : bond 0.00358 (10755) covalent geometry : angle 0.54747 (14711) *********************** 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 120 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 1.037 Fit side-chains REVERT: 2 29 GLU cc_start: 0.6409 (mp0) cc_final: 0.6104 (mp0) REVERT: 2 43 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.7623 (tttt) REVERT: 2 227 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6400 (mp0) REVERT: 2 233 ILE cc_start: 0.7796 (pt) cc_final: 0.7574 (pt) REVERT: 2 375 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6188 (tm-30) REVERT: 2 410 MET cc_start: 0.6593 (tpt) cc_final: 0.5833 (tpt) REVERT: 2 414 ASN cc_start: 0.7773 (t0) cc_final: 0.7304 (t0) REVERT: 2 417 ARG cc_start: 0.8265 (ttp-170) cc_final: 0.7815 (ttm170) REVERT: 2 427 LYS cc_start: 0.7800 (ttmt) cc_final: 0.7557 (ttpt) REVERT: 3 72 MET cc_start: 0.8342 (OUTLIER) cc_final: 0.7600 (ttt) REVERT: 3 263 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6399 (mt) REVERT: 3 434 TYR cc_start: 0.8534 (m-80) cc_final: 0.7519 (m-80) outliers start: 21 outliers final: 7 residues processed: 114 average time/residue: 1.1144 time to fit residues: 138.7628 Evaluate side-chains 106 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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 227 GLU 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 263 LEU 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 110 optimal weight: 0.2980 chunk 147 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 113 optimal weight: 0.4980 chunk 140 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 64 optimal weight: 30.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 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 = 0.231811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.149675 restraints weight = 11207.209| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 3.20 r_work: 0.3335 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10775 Z= 0.140 Angle : 0.541 10.407 14753 Z= 0.270 Chirality : 0.041 0.146 1725 Planarity : 0.004 0.078 1930 Dihedral : 4.079 53.983 1685 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.27 % Allowed : 14.38 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1486 helix: 2.22 (0.20), residues: 668 sheet: -1.23 (0.45), residues: 156 loop : -2.11 (0.22), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 520 HIS 0.003 0.001 HIS 3 94 PHE 0.012 0.001 PHE 3 195 TYR 0.023 0.001 TYR 3 318 ARG 0.018 0.000 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00035 ( 2) link_NAG-ASN : angle 0.96131 ( 6) hydrogen bonds : bond 0.03461 ( 541) hydrogen bonds : angle 3.78472 ( 1581) SS BOND : bond 0.00176 ( 18) SS BOND : angle 0.47523 ( 36) covalent geometry : bond 0.00332 (10755) covalent geometry : angle 0.54094 (14711) *********************** 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 116 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 1.128 Fit side-chains revert: symmetry clash REVERT: 2 29 GLU cc_start: 0.6422 (mp0) cc_final: 0.6054 (mp0) REVERT: 2 43 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7532 (tttt) REVERT: 2 227 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6437 (mp0) REVERT: 2 233 ILE cc_start: 0.7631 (pt) cc_final: 0.7419 (pt) REVERT: 2 375 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.6302 (tm-30) REVERT: 2 410 MET cc_start: 0.6512 (tpt) cc_final: 0.5724 (tpt) REVERT: 2 414 ASN cc_start: 0.7854 (t0) cc_final: 0.7400 (t0) REVERT: 2 417 ARG cc_start: 0.8112 (ttp-170) cc_final: 0.7699 (ttm170) REVERT: 2 427 LYS cc_start: 0.7889 (ttmt) cc_final: 0.7580 (ttpt) REVERT: 2 476 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7746 (mm-30) REVERT: 3 72 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7654 (ttt) REVERT: 3 203 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7624 (mt-10) REVERT: 3 235 ARG cc_start: 0.7100 (ttm110) cc_final: 0.6651 (mtt-85) REVERT: 3 263 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6191 (mt) REVERT: 3 434 TYR cc_start: 0.8618 (m-80) cc_final: 0.7550 (m-80) outliers start: 21 outliers final: 10 residues processed: 108 average time/residue: 1.0691 time to fit residues: 127.2624 Evaluate side-chains 108 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 191 VAL 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 79 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 108 optimal weight: 0.0370 chunk 112 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 147 optimal weight: 7.9990 chunk 55 optimal weight: 40.0000 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 117 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 overall best weight: 0.7618 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.228023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.150531 restraints weight = 11025.692| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.44 r_work: 0.3379 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10775 Z= 0.164 Angle : 0.567 10.054 14753 Z= 0.283 Chirality : 0.042 0.158 1725 Planarity : 0.004 0.089 1930 Dihedral : 4.191 53.769 1685 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.16 % Allowed : 14.59 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1486 helix: 2.20 (0.20), residues: 667 sheet: -1.34 (0.44), residues: 156 loop : -2.15 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 3 303 HIS 0.004 0.001 HIS 3 94 PHE 0.013 0.002 PHE 3 195 TYR 0.024 0.001 TYR 3 318 ARG 0.018 0.001 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00059 ( 2) link_NAG-ASN : angle 0.93868 ( 6) hydrogen bonds : bond 0.03630 ( 541) hydrogen bonds : angle 3.81407 ( 1581) SS BOND : bond 0.00203 ( 18) SS BOND : angle 0.53130 ( 36) covalent geometry : bond 0.00392 (10755) covalent geometry : angle 0.56695 (14711) ********************** 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: 20 poor density : 97 time to evaluate : 1.707 Fit side-chains revert: symmetry clash REVERT: 2 29 GLU cc_start: 0.6540 (mp0) cc_final: 0.6204 (mp0) REVERT: 2 43 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.7564 (tttt) REVERT: 2 227 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: 2 269 PHE cc_start: 0.8458 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: 2 375 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6308 (tm-30) REVERT: 2 410 MET cc_start: 0.6527 (tpt) cc_final: 0.5640 (tpt) REVERT: 2 414 ASN cc_start: 0.7782 (t0) cc_final: 0.7248 (t0) REVERT: 2 417 ARG cc_start: 0.8166 (ttp-170) cc_final: 0.7768 (ttm170) REVERT: 2 427 LYS cc_start: 0.7979 (ttmt) cc_final: 0.7692 (ttpt) REVERT: 2 476 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7768 (mm-30) REVERT: 3 72 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7636 (ttt) REVERT: 3 203 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7302 (mm-30) REVERT: 3 235 ARG cc_start: 0.7204 (ttm110) cc_final: 0.6728 (mtt-85) REVERT: 3 263 LEU cc_start: 0.6679 (OUTLIER) cc_final: 0.6425 (mt) REVERT: 3 283 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: 3 434 TYR cc_start: 0.8580 (m-80) cc_final: 0.7551 (m-80) outliers start: 20 outliers final: 9 residues processed: 112 average time/residue: 1.3383 time to fit residues: 164.7327 Evaluate side-chains 111 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 269 PHE 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 263 LEU Chi-restraints excluded: chain 3 residue 283 GLU 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 45 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 54 optimal weight: 8.9990 chunk 86 optimal weight: 0.9980 chunk 96 optimal weight: 1.9990 chunk 122 optimal weight: 0.5980 chunk 142 optimal weight: 20.0000 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 3 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.226439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.147453 restraints weight = 11005.179| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.72 r_work: 0.3269 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 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 : 0.005 0.054 10775 Z= 0.211 Angle : 0.608 10.031 14753 Z= 0.306 Chirality : 0.044 0.168 1725 Planarity : 0.004 0.084 1930 Dihedral : 4.420 53.194 1685 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.95 % Allowed : 14.81 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1486 helix: 2.10 (0.20), residues: 667 sheet: -1.52 (0.43), residues: 156 loop : -2.22 (0.22), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 3 303 HIS 0.005 0.001 HIS 3 94 PHE 0.014 0.002 PHE 2 224 TYR 0.025 0.002 TYR 3 318 ARG 0.018 0.001 ARG 3 235 Details of bonding type rmsd link_NAG-ASN : bond 0.00141 ( 2) link_NAG-ASN : angle 1.05327 ( 6) hydrogen bonds : bond 0.03937 ( 541) hydrogen bonds : angle 3.92315 ( 1581) SS BOND : bond 0.00250 ( 18) SS BOND : angle 0.63262 ( 36) covalent geometry : bond 0.00509 (10755) covalent geometry : angle 0.60768 (14711) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8798.46 seconds wall clock time: 157 minutes 6.09 seconds (9426.09 seconds total)