Starting phenix.real_space_refine on Sat Aug 23 08:42:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcv_36166/08_2025/8jcv_36166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcv_36166/08_2025/8jcv_36166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jcv_36166/08_2025/8jcv_36166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcv_36166/08_2025/8jcv_36166.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jcv_36166/08_2025/8jcv_36166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcv_36166/08_2025/8jcv_36166.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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 62 5.16 5 C 6682 2.51 5 N 1891 2.21 5 O 2032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 10667 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5283 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 179} Link IDs: {'PTRANS': 37, 'TRANS': 725} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 683 Unresolved non-hydrogen angles: 885 Unresolved non-hydrogen dihedrals: 575 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLU:plan': 12, 'ARG:plan': 13, 'ASN:plan1': 5, 'ASP:plan': 7, 'GLN:plan1': 7, 'TRP:plan': 5, 'TYR:plan': 10, 'PHE:plan': 12, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 369 Chain: "3" Number of atoms: 5304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5304 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 171} Link IDs: {'PTRANS': 29, 'TRANS': 721} Chain breaks: 3 Unresolved non-hydrogen bonds: 682 Unresolved non-hydrogen angles: 874 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 69 Planarities with less than four sites: {'GLU:plan': 8, 'ASN:plan1': 9, 'ASP:plan': 6, 'ARG:plan': 12, 'GLN:plan1': 3, 'HIS:plan': 3, 'TRP:plan': 4, 'PHE:plan': 16, 'TYR:plan': 9} Unresolved non-hydrogen planarities: 355 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: 3.07, per 1000 atoms: 0.29 Number of scatterers: 10667 At special positions: 0 Unit cell: (84.609, 122.094, 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 62 16.00 O 2032 8.00 N 1891 7.00 C 6682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, 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 3 361 " - 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: 0.96 Conformation dependent library (CDL) restraints added in 568.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2842 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 48.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain '2' and resid 58 through 75 Processing helix chain '2' and resid 94 through 103 Processing helix chain '2' and resid 104 through 106 No H-bonds generated for 'chain '2' and resid 104 through 106' Processing helix chain '2' and resid 145 through 159 removed outlier: 4.296A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N PHE 2 158 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) Processing helix chain '2' and resid 170 through 174 Processing helix chain '2' and resid 189 through 202 Processing helix chain '2' and resid 218 through 231 removed outlier: 3.517A pdb=" N GLU 2 222 " --> pdb=" O GLU 2 218 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA 2 230 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG 2 231 " --> pdb=" O GLU 2 227 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 260 removed outlier: 4.285A pdb=" N LYS 2 260 " --> pdb=" O ALA 2 256 " (cutoff:3.500A) Processing helix chain '2' and resid 271 through 285 Processing helix chain '2' and resid 300 through 305 removed outlier: 4.103A pdb=" N VAL 2 304 " --> pdb=" O LEU 2 300 " (cutoff:3.500A) Processing helix chain '2' and resid 324 through 332 Processing helix chain '2' and resid 344 through 353 Processing helix chain '2' and resid 360 through 364 removed outlier: 3.517A pdb=" N ALA 2 363 " --> pdb=" O ARG 2 360 " (cutoff:3.500A) Processing helix chain '2' and resid 375 through 377 No H-bonds generated for 'chain '2' and resid 375 through 377' Processing helix chain '2' and resid 378 through 400 removed outlier: 3.570A pdb=" N VAL 2 382 " --> pdb=" O ILE 2 378 " (cutoff:3.500A) Processing helix chain '2' and resid 407 through 411 removed outlier: 3.814A pdb=" N MET 2 410 " --> pdb=" O CYS 2 407 " (cutoff:3.500A) Processing helix chain '2' and resid 414 through 422 removed outlier: 3.697A pdb=" N LEU 2 418 " --> pdb=" O ASN 2 414 " (cutoff:3.500A) Processing helix chain '2' and resid 423 through 426 removed outlier: 3.990A pdb=" N VAL 2 426 " --> pdb=" O VAL 2 423 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 423 through 426' Processing helix chain '2' and resid 482 through 485 Processing helix chain '2' and resid 568 through 592 removed outlier: 3.848A pdb=" N THR 2 573 " --> pdb=" O VAL 2 569 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL 2 588 " --> pdb=" O PHE 2 584 " (cutoff:3.500A) Processing helix chain '2' and resid 595 through 601 removed outlier: 3.502A pdb=" N ALA 2 600 " --> pdb=" O PRO 2 596 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER 2 601 " --> pdb=" O VAL 2 597 " (cutoff:3.500A) Processing helix chain '2' and resid 602 through 623 Processing helix chain '2' and resid 631 through 660 removed outlier: 4.333A pdb=" N ARG 2 656 " --> pdb=" O THR 2 652 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE 2 657 " --> pdb=" O LYS 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 702 removed outlier: 3.974A pdb=" N VAL 2 699 " --> pdb=" O VAL 2 695 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA 2 702 " --> pdb=" O LEU 2 698 " (cutoff:3.500A) Processing helix chain '2' and resid 723 through 749 removed outlier: 3.776A pdb=" N SER 2 727 " --> pdb=" O HIS 2 723 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLY 2 730 " --> pdb=" O ALA 2 726 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER 2 731 " --> pdb=" O SER 2 727 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS 2 748 " --> pdb=" O LEU 2 744 " (cutoff:3.500A) Processing helix chain '2' and resid 757 through 784 removed outlier: 4.264A pdb=" N PHE 2 761 " --> pdb=" O ASN 2 757 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE 2 771 " --> pdb=" O TYR 2 767 " (cutoff:3.500A) Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 786 through 818 removed outlier: 4.017A pdb=" N ALA 2 811 " --> pdb=" O GLY 2 807 " (cutoff:3.500A) Proline residue: 2 812 - end of helix Processing helix chain '3' and resid 65 through 82 Processing helix chain '3' and resid 101 through 109 Processing helix chain '3' and resid 109 through 115 removed outlier: 3.760A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) Processing helix chain '3' and resid 150 through 164 removed outlier: 3.996A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE 3 164 " --> pdb=" O LEU 3 160 " (cutoff:3.500A) Processing helix chain '3' and resid 176 through 180 Processing helix chain '3' and resid 194 through 208 removed outlier: 3.673A pdb=" N ALA 3 198 " --> pdb=" O ASP 3 194 " (cutoff:3.500A) Processing helix chain '3' and resid 220 through 238 removed outlier: 3.715A pdb=" N LEU 3 236 " --> pdb=" O GLN 3 232 " (cutoff:3.500A) Processing helix chain '3' and resid 252 through 265 removed outlier: 3.557A pdb=" N GLN 3 265 " --> pdb=" O ARG 3 261 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 290 removed outlier: 4.057A pdb=" N ARG 3 282 " --> pdb=" O SER 3 278 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N GLU 3 283 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG 3 290 " --> pdb=" O ALA 3 286 " (cutoff:3.500A) Processing helix chain '3' and resid 330 through 339 removed outlier: 3.604A pdb=" N ASP 3 334 " --> pdb=" O VAL 3 330 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER 3 339 " --> pdb=" O ARG 3 335 " (cutoff:3.500A) Processing helix chain '3' and resid 349 through 360 removed outlier: 4.308A pdb=" N ASP 3 353 " --> pdb=" O PRO 3 349 " (cutoff:3.500A) Processing helix chain '3' and resid 380 through 384 removed outlier: 3.520A pdb=" N ASN 3 383 " --> pdb=" O ASP 3 380 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR 3 384 " --> pdb=" O SER 3 381 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 380 through 384' Processing helix chain '3' and resid 389 through 412 removed outlier: 3.712A pdb=" N MET 3 400 " --> pdb=" O ALA 3 396 " (cutoff:3.500A) Processing helix chain '3' and resid 426 through 433 removed outlier: 3.515A pdb=" N ASP 3 433 " --> pdb=" O LYS 3 429 " (cutoff:3.500A) Processing helix chain '3' and resid 577 through 601 Processing helix chain '3' and resid 614 through 632 removed outlier: 3.501A pdb=" N CYS 3 627 " --> pdb=" O GLY 3 623 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE 3 632 " --> pdb=" O MET 3 628 " (cutoff:3.500A) Processing helix chain '3' and resid 639 through 665 removed outlier: 4.100A pdb=" N LEU 3 659 " --> pdb=" O CYS 3 655 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU 3 660 " --> pdb=" O TYR 3 656 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR 3 661 " --> pdb=" O SER 3 657 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LYS 3 662 " --> pdb=" O ALA 3 658 " (cutoff:3.500A) Processing helix chain '3' and resid 685 through 706 removed outlier: 3.757A pdb=" N VAL 3 703 " --> pdb=" O GLN 3 699 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER 3 704 " --> pdb=" O ILE 3 700 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP 3 706 " --> pdb=" O MET 3 702 " (cutoff:3.500A) Processing helix chain '3' and resid 732 through 759 removed outlier: 3.765A pdb=" N SER 3 736 " --> pdb=" O VAL 3 732 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE 3 739 " --> pdb=" O SER 3 735 " (cutoff:3.500A) Processing helix chain '3' and resid 764 through 791 Proline residue: 3 787 - end of helix removed outlier: 3.526A pdb=" N TYR 3 790 " --> pdb=" O LEU 3 786 " (cutoff:3.500A) Processing helix chain '3' and resid 797 through 825 removed outlier: 3.598A pdb=" N ALA 3 820 " --> pdb=" O GLY 3 816 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id=AA1, first strand: chain '2' and resid 26 through 27 removed outlier: 6.611A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 162 through 164 Processing sheet with id=AA3, first strand: chain '2' and resid 234 through 235 removed outlier: 3.906A pdb=" N VAL 2 207 " --> pdb=" O CYS 2 234 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR 2 206 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL 2 267 " --> pdb=" O TYR 2 206 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER 2 208 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA 2 266 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N TRP 2 291 " --> pdb=" O ILE 2 315 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE 2 317 " --> pdb=" O TRP 2 291 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N ALA 2 293 " --> pdb=" O ILE 2 317 " (cutoff:3.500A) removed outlier: 9.394A pdb=" N LEU 2 319 " --> pdb=" O ALA 2 293 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR 2 479 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 428 through 429 removed outlier: 3.830A pdb=" N PHE 2 428 " --> pdb=" O VAL 2 441 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 32 through 35 removed outlier: 3.610A pdb=" N ILE 3 33 " --> pdb=" O ILE 3 95 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL 3 93 " --> pdb=" O ILE 3 35 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY 3 144 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU 3 44 " --> pdb=" O ILE 3 146 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL 3 145 " --> pdb=" O ILE 3 169 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 48 through 50 removed outlier: 4.794A pdb=" N ARG 3 59 " --> pdb=" O GLU 3 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 240 through 247 removed outlier: 9.647A pdb=" N VAL 3 213 " --> pdb=" O THR 3 243 " (cutoff:3.500A) removed outlier: 8.957A pdb=" N GLU 3 245 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR 3 215 " --> pdb=" O GLU 3 245 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N VAL 3 247 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA 3 217 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N TYR 3 212 " --> pdb=" O VAL 3 271 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N VAL 3 273 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER 3 214 " --> pdb=" O VAL 3 273 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE 3 275 " --> pdb=" O SER 3 214 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N VAL 3 216 " --> pdb=" O PHE 3 275 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL 3 272 " --> pdb=" O VAL 3 298 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain '3' and resid 321 through 325 removed outlier: 6.564A pdb=" N TYR 3 466 " --> pdb=" O HIS 3 485 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N HIS 3 485 " --> pdb=" O TYR 3 466 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL 3 468 " --> pdb=" O VAL 3 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 440 through 441 removed outlier: 3.721A pdb=" N PHE 3 440 " --> pdb=" O VAL 3 454 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 518 through 521 removed outlier: 3.785A pdb=" N ILE 3 530 " --> pdb=" O MET 3 521 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1536 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: 1.62 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3431 1.34 - 1.46: 1997 1.46 - 1.58: 5374 1.58 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 10880 Sorted by residual: bond pdb=" CAT Z99 22101 " pdb=" OAP Z99 22101 " ideal model delta sigma weight residual 1.364 1.451 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" CAT Z99 32101 " pdb=" OAP Z99 32101 " ideal model delta sigma weight residual 1.364 1.450 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" CAS Z99 22101 " pdb=" OAP Z99 22101 " ideal model delta sigma weight residual 1.369 1.452 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CAS Z99 32101 " pdb=" OAP Z99 32101 " ideal model delta sigma weight residual 1.369 1.449 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CA ALA 3 172 " pdb=" CB ALA 3 172 " ideal model delta sigma weight residual 1.535 1.498 0.037 1.64e-02 3.72e+03 5.06e+00 ... (remaining 10875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 14503 1.50 - 3.00: 280 3.00 - 4.50: 50 4.50 - 6.00: 25 6.00 - 7.50: 12 Bond angle restraints: 14870 Sorted by residual: angle pdb=" C ARG 2 358 " pdb=" N GLN 2 359 " pdb=" CA GLN 2 359 " ideal model delta sigma weight residual 121.40 126.72 -5.32 1.52e+00 4.33e-01 1.23e+01 angle pdb=" N ARG 2 360 " pdb=" CA ARG 2 360 " pdb=" C ARG 2 360 " ideal model delta sigma weight residual 107.73 112.25 -4.52 1.34e+00 5.57e-01 1.14e+01 angle pdb=" C SER 2 340 " pdb=" N ARG 2 341 " pdb=" CA ARG 2 341 " ideal model delta sigma weight residual 120.38 124.95 -4.57 1.37e+00 5.33e-01 1.11e+01 angle pdb=" C ASP 2 215 " pdb=" N TYR 2 216 " pdb=" CA TYR 2 216 " ideal model delta sigma weight residual 121.54 127.56 -6.02 1.91e+00 2.74e-01 9.95e+00 angle pdb=" CA PRO 2 76 " pdb=" C PRO 2 76 " pdb=" N HIS 2 77 " ideal model delta sigma weight residual 116.45 118.78 -2.33 8.50e-01 1.38e+00 7.49e+00 ... (remaining 14865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.55: 6411 34.55 - 69.09: 117 69.09 - 103.64: 20 103.64 - 138.19: 7 138.19 - 172.73: 2 Dihedral angle restraints: 6557 sinusoidal: 2167 harmonic: 4390 Sorted by residual: dihedral pdb=" CB CYS 2 234 " pdb=" SG CYS 2 234 " pdb=" SG CYS 2 518 " pdb=" CB CYS 2 518 " ideal model delta sinusoidal sigma weight residual -86.00 -161.06 75.06 1 1.00e+01 1.00e-02 7.13e+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 93.00 26.23 66.77 1 1.00e+01 1.00e-02 5.81e+01 dihedral pdb=" CB CYS 2 500 " pdb=" SG CYS 2 500 " pdb=" SG CYS 2 519 " pdb=" CB CYS 2 519 " ideal model delta sinusoidal sigma weight residual 93.00 29.54 63.46 1 1.00e+01 1.00e-02 5.31e+01 ... (remaining 6554 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.071: 1723 1.071 - 2.143: 0 2.143 - 3.214: 0 3.214 - 4.286: 0 4.286 - 5.357: 2 Chirality restraints: 1725 Sorted by residual: chirality pdb=" CAW Z99 32101 " pdb=" CAN Z99 32101 " pdb=" CAU Z99 32101 " pdb=" CAV Z99 32101 " both_signs ideal model delta sigma weight residual False 2.61 -2.75 5.36 2.00e-01 2.50e+01 7.18e+02 chirality pdb=" CAW Z99 22101 " pdb=" CAN Z99 22101 " pdb=" CAU Z99 22101 " pdb=" CAV Z99 22101 " both_signs ideal model delta sigma weight residual False 2.61 -2.64 5.25 2.00e-01 2.50e+01 6.89e+02 chirality pdb=" CAZ Z99 22101 " pdb=" CAO Z99 22101 " pdb=" CAX Z99 22101 " pdb=" CAY Z99 22101 " both_signs ideal model delta sigma weight residual True 2.39 -2.74 -0.35 2.00e-01 2.50e+01 3.07e+00 ... (remaining 1722 not shown) Planarity restraints: 1971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP 2 75 " 0.063 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO 2 76 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO 2 76 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO 2 76 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL 2 370 " 0.025 5.00e-02 4.00e+02 3.77e-02 2.28e+00 pdb=" N PRO 2 371 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO 2 371 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO 2 371 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG 2 74 " -0.110 9.50e-02 1.11e+02 4.94e-02 1.81e+00 pdb=" NE ARG 2 74 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG 2 74 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG 2 74 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG 2 74 " -0.001 2.00e-02 2.50e+03 ... (remaining 1968 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3235 2.82 - 3.34: 10329 3.34 - 3.86: 16956 3.86 - 4.38: 18372 4.38 - 4.90: 32263 Nonbonded interactions: 81155 Sorted by model distance: nonbonded pdb=" NE2 GLN 3 508 " pdb=" O CYS 3 509 " model vdw 2.300 3.120 nonbonded pdb=" NH1 ARG 2 460 " pdb=" O ALA 2 461 " model vdw 2.307 3.120 nonbonded pdb=" O LEU 3 39 " pdb=" N GLY 3 92 " model vdw 2.314 3.120 nonbonded pdb=" NH2 ARG 2 200 " pdb=" O ARG 2 231 " model vdw 2.328 3.120 nonbonded pdb=" O SER 3 255 " pdb=" OG SER 3 258 " model vdw 2.350 3.040 ... (remaining 81150 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=0.08 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: 3.420 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.890 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 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 0.087 10899 Z= 0.153 Angle : 0.562 7.501 14910 Z= 0.277 Chirality : 0.186 5.357 1725 Planarity : 0.004 0.098 1969 Dihedral : 14.870 172.733 3664 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.11 % Allowed : 0.43 % Favored : 99.46 % 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: 1.15 (0.22), residues: 1500 helix: 2.85 (0.20), residues: 635 sheet: 0.13 (0.49), residues: 132 loop : -1.09 (0.23), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG 2 74 TYR 0.010 0.001 TYR 3 478 PHE 0.010 0.001 PHE 2 250 TRP 0.015 0.001 TRP 3 554 HIS 0.005 0.000 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00306 (10880) covalent geometry : angle 0.56105 (14870) SS BOND : bond 0.00179 ( 17) SS BOND : angle 0.99131 ( 34) hydrogen bonds : bond 0.22306 ( 523) hydrogen bonds : angle 5.81387 ( 1536) link_NAG-ASN : bond 0.00068 ( 2) link_NAG-ASN : angle 0.75579 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.445 Fit side-chains revert: symmetry clash REVERT: 2 250 PHE cc_start: 0.6027 (m-10) cc_final: 0.5815 (m-10) REVERT: 2 410 MET cc_start: 0.6932 (ppp) cc_final: 0.6662 (ppp) REVERT: 3 422 MET cc_start: 0.5571 (ttp) cc_final: 0.5050 (ttp) REVERT: 3 537 TYR cc_start: 0.6835 (p90) cc_final: 0.6511 (p90) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.1302 time to fit residues: 21.6890 Evaluate side-chains 90 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 0.3980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 9.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 162 GLN 2 425 ASN 2 655 ASN 3 67 GLN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 405 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.189402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.133460 restraints weight = 17093.804| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 3.95 r_work: 0.3496 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3503 r_free = 0.3503 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 10899 Z= 0.262 Angle : 0.651 12.239 14910 Z= 0.338 Chirality : 0.045 0.236 1725 Planarity : 0.005 0.066 1969 Dihedral : 5.210 37.254 1706 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.18 % Allowed : 8.71 % Favored : 90.11 % 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: 0.83 (0.22), residues: 1500 helix: 2.48 (0.20), residues: 653 sheet: -0.46 (0.44), residues: 140 loop : -1.15 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG 2 156 TYR 0.020 0.002 TYR 3 256 PHE 0.024 0.002 PHE 2 327 TRP 0.020 0.002 TRP 3 529 HIS 0.005 0.001 HIS 2 87 Details of bonding type rmsd covalent geometry : bond 0.00606 (10880) covalent geometry : angle 0.64787 (14870) SS BOND : bond 0.00217 ( 17) SS BOND : angle 1.28114 ( 34) hydrogen bonds : bond 0.04799 ( 523) hydrogen bonds : angle 4.20801 ( 1536) link_NAG-ASN : bond 0.00291 ( 2) link_NAG-ASN : angle 1.83894 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.499 Fit side-chains REVERT: 2 245 MET cc_start: 0.5003 (OUTLIER) cc_final: 0.4244 (tmm) REVERT: 2 250 PHE cc_start: 0.6309 (m-10) cc_final: 0.5942 (m-10) REVERT: 2 410 MET cc_start: 0.6988 (ppp) cc_final: 0.6383 (ppp) REVERT: 3 49 GLU cc_start: 0.7345 (mt-10) cc_final: 0.6960 (mt-10) REVERT: 3 270 ARG cc_start: 0.6983 (mtm-85) cc_final: 0.6726 (ptp90) outliers start: 11 outliers final: 7 residues processed: 108 average time/residue: 0.1257 time to fit residues: 18.8109 Evaluate side-chains 96 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 158 PHE Chi-restraints excluded: chain 2 residue 195 MET Chi-restraints excluded: chain 2 residue 198 ILE Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 292 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 77 optimal weight: 0.5980 chunk 70 optimal weight: 30.0000 chunk 119 optimal weight: 0.6980 chunk 66 optimal weight: 20.0000 chunk 57 optimal weight: 30.0000 chunk 15 optimal weight: 0.7980 chunk 132 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 90 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 351 GLN 2 425 ASN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4549 r_free = 0.4549 target = 0.191198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.129854 restraints weight = 17259.788| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 3.79 r_work: 0.3503 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10899 Z= 0.137 Angle : 0.527 9.041 14910 Z= 0.266 Chirality : 0.041 0.160 1725 Planarity : 0.004 0.063 1969 Dihedral : 4.637 30.545 1706 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.29 % Allowed : 10.97 % Favored : 87.74 % 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: 0.85 (0.22), residues: 1500 helix: 2.59 (0.20), residues: 655 sheet: -0.82 (0.42), residues: 138 loop : -1.18 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 445 TYR 0.012 0.001 TYR 3 256 PHE 0.013 0.001 PHE 2 327 TRP 0.008 0.001 TRP 3 554 HIS 0.004 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00314 (10880) covalent geometry : angle 0.52521 (14870) SS BOND : bond 0.00190 ( 17) SS BOND : angle 0.84339 ( 34) hydrogen bonds : bond 0.03946 ( 523) hydrogen bonds : angle 3.84542 ( 1536) link_NAG-ASN : bond 0.00054 ( 2) link_NAG-ASN : angle 1.41131 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.403 Fit side-chains REVERT: 2 216 TYR cc_start: 0.8484 (t80) cc_final: 0.8273 (t80) REVERT: 2 245 MET cc_start: 0.5016 (OUTLIER) cc_final: 0.4259 (tmm) REVERT: 2 250 PHE cc_start: 0.6228 (m-10) cc_final: 0.5900 (m-10) REVERT: 2 334 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7694 (mp) REVERT: 2 410 MET cc_start: 0.6666 (ppp) cc_final: 0.6279 (ppp) REVERT: 2 445 ARG cc_start: 0.8237 (ptp90) cc_final: 0.7955 (ptp90) REVERT: 2 466 TYR cc_start: 0.7267 (m-10) cc_final: 0.6832 (m-10) REVERT: 3 49 GLU cc_start: 0.7255 (mt-10) cc_final: 0.6839 (mt-10) REVERT: 3 239 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6384 (mp) REVERT: 3 331 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7398 (mmp-170) outliers start: 12 outliers final: 6 residues processed: 102 average time/residue: 0.1147 time to fit residues: 16.5258 Evaluate side-chains 93 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 195 MET Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 285 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 67 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 54 optimal weight: 20.0000 chunk 80 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 125 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 128 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 351 GLN 2 425 ASN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.190003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.133395 restraints weight = 17431.502| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.54 r_work: 0.3463 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10899 Z= 0.151 Angle : 0.528 8.398 14910 Z= 0.270 Chirality : 0.041 0.162 1725 Planarity : 0.004 0.067 1969 Dihedral : 4.590 27.310 1706 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.51 % Allowed : 12.37 % Favored : 86.13 % 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: 0.79 (0.22), residues: 1500 helix: 2.57 (0.20), residues: 657 sheet: -1.02 (0.40), residues: 138 loop : -1.21 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 445 TYR 0.012 0.001 TYR 3 256 PHE 0.017 0.001 PHE 2 327 TRP 0.006 0.001 TRP 2 291 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00354 (10880) covalent geometry : angle 0.52732 (14870) SS BOND : bond 0.00152 ( 17) SS BOND : angle 0.62745 ( 34) hydrogen bonds : bond 0.03599 ( 523) hydrogen bonds : angle 3.70621 ( 1536) link_NAG-ASN : bond 0.00202 ( 2) link_NAG-ASN : angle 1.49378 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 88 time to evaluate : 0.419 Fit side-chains REVERT: 2 216 TYR cc_start: 0.8551 (t80) cc_final: 0.8313 (t80) REVERT: 2 245 MET cc_start: 0.5201 (OUTLIER) cc_final: 0.4408 (tmm) REVERT: 2 334 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7656 (mp) REVERT: 2 445 ARG cc_start: 0.8402 (ptp90) cc_final: 0.8130 (ptp90) REVERT: 2 466 TYR cc_start: 0.7327 (m-10) cc_final: 0.6958 (m-10) REVERT: 3 239 ILE cc_start: 0.6843 (OUTLIER) cc_final: 0.6460 (mp) REVERT: 3 331 ARG cc_start: 0.7845 (mtt90) cc_final: 0.7370 (mmp-170) outliers start: 14 outliers final: 9 residues processed: 98 average time/residue: 0.1130 time to fit residues: 15.8406 Evaluate side-chains 94 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 281 SER Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 315 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 26 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 70 optimal weight: 30.0000 chunk 138 optimal weight: 9.9990 chunk 54 optimal weight: 20.0000 chunk 148 optimal weight: 0.0570 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 425 ASN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.189675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.132684 restraints weight = 17189.987| |-----------------------------------------------------------------------------| r_work (start): 0.3846 rms_B_bonded: 3.48 r_work: 0.3519 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10899 Z= 0.148 Angle : 0.523 7.773 14910 Z= 0.266 Chirality : 0.041 0.160 1725 Planarity : 0.004 0.068 1969 Dihedral : 4.480 31.250 1706 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.94 % Allowed : 13.12 % Favored : 84.95 % 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: 0.82 (0.22), residues: 1500 helix: 2.63 (0.19), residues: 663 sheet: -1.15 (0.41), residues: 138 loop : -1.24 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 156 TYR 0.011 0.001 TYR 3 256 PHE 0.015 0.001 PHE 2 327 TRP 0.024 0.001 TRP 2 349 HIS 0.004 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00347 (10880) covalent geometry : angle 0.52224 (14870) SS BOND : bond 0.00155 ( 17) SS BOND : angle 0.58020 ( 34) hydrogen bonds : bond 0.03417 ( 523) hydrogen bonds : angle 3.63572 ( 1536) link_NAG-ASN : bond 0.00143 ( 2) link_NAG-ASN : angle 1.47859 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.504 Fit side-chains REVERT: 2 245 MET cc_start: 0.5459 (OUTLIER) cc_final: 0.4857 (tmm) REVERT: 2 334 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7695 (mp) REVERT: 3 38 ASP cc_start: 0.7158 (m-30) cc_final: 0.6814 (t70) REVERT: 3 239 ILE cc_start: 0.6888 (OUTLIER) cc_final: 0.6496 (mp) REVERT: 3 331 ARG cc_start: 0.7736 (mtt90) cc_final: 0.7350 (mmp-170) outliers start: 18 outliers final: 11 residues processed: 102 average time/residue: 0.1147 time to fit residues: 16.7199 Evaluate side-chains 100 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 281 SER Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 315 HIS Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 565 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 30.0000 chunk 115 optimal weight: 0.3980 chunk 144 optimal weight: 0.0040 chunk 32 optimal weight: 0.4980 chunk 145 optimal weight: 10.0000 chunk 63 optimal weight: 20.0000 chunk 117 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 162 GLN 2 425 ASN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.190784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.134757 restraints weight = 17321.282| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 3.69 r_work: 0.3508 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10899 Z= 0.113 Angle : 0.500 6.486 14910 Z= 0.254 Chirality : 0.040 0.146 1725 Planarity : 0.003 0.072 1969 Dihedral : 4.324 31.188 1706 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.29 % Allowed : 14.84 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.22), residues: 1500 helix: 2.73 (0.19), residues: 663 sheet: -1.07 (0.41), residues: 138 loop : -1.20 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 445 TYR 0.010 0.001 TYR 3 256 PHE 0.010 0.001 PHE 2 327 TRP 0.033 0.001 TRP 2 349 HIS 0.003 0.000 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00262 (10880) covalent geometry : angle 0.49917 (14870) SS BOND : bond 0.00161 ( 17) SS BOND : angle 0.58159 ( 34) hydrogen bonds : bond 0.03171 ( 523) hydrogen bonds : angle 3.54804 ( 1536) link_NAG-ASN : bond 0.00081 ( 2) link_NAG-ASN : angle 1.32495 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5574 (OUTLIER) cc_final: 0.4957 (tmm) REVERT: 2 334 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7557 (mp) REVERT: 2 445 ARG cc_start: 0.8212 (ptp90) cc_final: 0.7914 (ptp90) REVERT: 2 466 TYR cc_start: 0.7367 (m-10) cc_final: 0.6981 (m-10) REVERT: 3 38 ASP cc_start: 0.7154 (m-30) cc_final: 0.6801 (t0) REVERT: 3 72 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8136 (ttt) outliers start: 12 outliers final: 9 residues processed: 102 average time/residue: 0.1150 time to fit residues: 17.1743 Evaluate side-chains 97 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 85 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 281 SER Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 52 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 56 optimal weight: 30.0000 chunk 61 optimal weight: 30.0000 chunk 101 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 162 GLN 2 425 ASN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.190141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.130314 restraints weight = 17166.607| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 4.05 r_work: 0.3465 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10899 Z= 0.129 Angle : 0.513 7.616 14910 Z= 0.259 Chirality : 0.041 0.155 1725 Planarity : 0.003 0.072 1969 Dihedral : 4.297 31.992 1706 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.94 % Allowed : 14.41 % Favored : 83.66 % 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: 0.93 (0.22), residues: 1500 helix: 2.74 (0.19), residues: 663 sheet: -1.08 (0.42), residues: 138 loop : -1.21 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 445 TYR 0.024 0.001 TYR 2 216 PHE 0.014 0.001 PHE 2 327 TRP 0.023 0.001 TRP 2 349 HIS 0.003 0.000 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00302 (10880) covalent geometry : angle 0.51260 (14870) SS BOND : bond 0.00178 ( 17) SS BOND : angle 0.54431 ( 34) hydrogen bonds : bond 0.03154 ( 523) hydrogen bonds : angle 3.54287 ( 1536) link_NAG-ASN : bond 0.00113 ( 2) link_NAG-ASN : angle 1.38832 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5642 (OUTLIER) cc_final: 0.5053 (tmm) REVERT: 2 334 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7568 (mp) REVERT: 2 445 ARG cc_start: 0.8375 (ptp90) cc_final: 0.8073 (ptp90) REVERT: 3 38 ASP cc_start: 0.7153 (m-30) cc_final: 0.6766 (t0) REVERT: 3 239 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6497 (mp) outliers start: 18 outliers final: 12 residues processed: 102 average time/residue: 0.1127 time to fit residues: 16.2866 Evaluate side-chains 102 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 281 SER Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 27 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 66 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 80 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 54 ASN 2 425 ASN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 731 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.188106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.125966 restraints weight = 17142.509| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 3.62 r_work: 0.3461 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10899 Z= 0.185 Angle : 0.564 9.476 14910 Z= 0.286 Chirality : 0.042 0.172 1725 Planarity : 0.004 0.077 1969 Dihedral : 4.449 35.282 1706 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.37 % Allowed : 14.52 % Favored : 83.12 % 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: 0.82 (0.22), residues: 1500 helix: 2.60 (0.19), residues: 671 sheet: -1.20 (0.42), residues: 138 loop : -1.24 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 445 TYR 0.025 0.001 TYR 2 216 PHE 0.017 0.002 PHE 2 327 TRP 0.015 0.001 TRP 2 349 HIS 0.004 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00437 (10880) covalent geometry : angle 0.56294 (14870) SS BOND : bond 0.00162 ( 17) SS BOND : angle 0.57279 ( 34) hydrogen bonds : bond 0.03396 ( 523) hydrogen bonds : angle 3.63698 ( 1536) link_NAG-ASN : bond 0.00263 ( 2) link_NAG-ASN : angle 1.61999 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.428 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5496 (OUTLIER) cc_final: 0.5055 (tmm) REVERT: 2 334 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7664 (mp) REVERT: 3 32 GLU cc_start: 0.7456 (pm20) cc_final: 0.7253 (pm20) REVERT: 3 72 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.8339 (ttt) REVERT: 3 239 ILE cc_start: 0.6858 (OUTLIER) cc_final: 0.6466 (mp) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 0.1111 time to fit residues: 17.0086 Evaluate side-chains 105 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 382 VAL Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 33 ILE Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 281 SER Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 52 optimal weight: 10.0000 chunk 29 optimal weight: 0.0040 chunk 46 optimal weight: 10.0000 chunk 65 optimal weight: 0.0970 chunk 143 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 110 optimal weight: 0.0970 chunk 8 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 162 GLN 2 425 ASN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.190695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.128337 restraints weight = 17283.475| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.74 r_work: 0.3501 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10899 Z= 0.105 Angle : 0.525 13.781 14910 Z= 0.262 Chirality : 0.040 0.140 1725 Planarity : 0.003 0.077 1969 Dihedral : 4.263 30.807 1706 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.61 % Allowed : 15.38 % Favored : 83.01 % 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: 0.94 (0.22), residues: 1500 helix: 2.70 (0.19), residues: 669 sheet: -0.94 (0.43), residues: 131 loop : -1.21 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 445 TYR 0.029 0.001 TYR 2 216 PHE 0.009 0.001 PHE 2 422 TRP 0.018 0.001 TRP 2 349 HIS 0.003 0.000 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00241 (10880) covalent geometry : angle 0.52451 (14870) SS BOND : bond 0.00183 ( 17) SS BOND : angle 0.59749 ( 34) hydrogen bonds : bond 0.03034 ( 523) hydrogen bonds : angle 3.56273 ( 1536) link_NAG-ASN : bond 0.00070 ( 2) link_NAG-ASN : angle 1.27354 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 180 TYR cc_start: 0.8407 (m-10) cc_final: 0.8137 (m-10) REVERT: 2 245 MET cc_start: 0.5379 (OUTLIER) cc_final: 0.4865 (tmm) REVERT: 2 334 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7500 (mp) REVERT: 2 445 ARG cc_start: 0.8266 (ptp90) cc_final: 0.7954 (ptp90) REVERT: 3 32 GLU cc_start: 0.7366 (pm20) cc_final: 0.7153 (pm20) REVERT: 3 72 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8192 (ttt) REVERT: 3 239 ILE cc_start: 0.6759 (OUTLIER) cc_final: 0.6334 (mp) REVERT: 3 437 LYS cc_start: 0.8507 (mmmt) cc_final: 0.8232 (mptt) outliers start: 15 outliers final: 10 residues processed: 107 average time/residue: 0.1134 time to fit residues: 17.1589 Evaluate side-chains 106 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 281 SER Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 73 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.0170 chunk 17 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 90 optimal weight: 0.0470 chunk 64 optimal weight: 7.9990 chunk 71 optimal weight: 30.0000 chunk 65 optimal weight: 0.0770 overall best weight: 0.3474 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 162 GLN 2 425 ASN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.191205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.132198 restraints weight = 17135.365| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 3.97 r_work: 0.3496 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10899 Z= 0.104 Angle : 0.513 10.232 14910 Z= 0.257 Chirality : 0.040 0.142 1725 Planarity : 0.003 0.076 1969 Dihedral : 4.153 26.610 1706 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.61 % Allowed : 15.27 % Favored : 83.12 % 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: 0.99 (0.22), residues: 1500 helix: 2.82 (0.19), residues: 664 sheet: -0.95 (0.44), residues: 131 loop : -1.23 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 2 445 TYR 0.009 0.001 TYR 3 104 PHE 0.009 0.001 PHE 2 422 TRP 0.016 0.001 TRP 2 349 HIS 0.003 0.000 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00239 (10880) covalent geometry : angle 0.51191 (14870) SS BOND : bond 0.00167 ( 17) SS BOND : angle 0.58106 ( 34) hydrogen bonds : bond 0.02958 ( 523) hydrogen bonds : angle 3.49849 ( 1536) link_NAG-ASN : bond 0.00066 ( 2) link_NAG-ASN : angle 1.22312 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5486 (OUTLIER) cc_final: 0.4922 (tmm) REVERT: 2 334 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7423 (mp) REVERT: 2 445 ARG cc_start: 0.8251 (ptp90) cc_final: 0.7919 (ptp90) REVERT: 3 32 GLU cc_start: 0.7397 (pm20) cc_final: 0.7195 (pm20) REVERT: 3 72 MET cc_start: 0.8546 (OUTLIER) cc_final: 0.8238 (ttt) REVERT: 3 239 ILE cc_start: 0.6763 (OUTLIER) cc_final: 0.6483 (mp) REVERT: 3 437 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8259 (mptt) outliers start: 15 outliers final: 11 residues processed: 105 average time/residue: 0.1102 time to fit residues: 16.1261 Evaluate side-chains 104 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 270 ARG Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 281 SER Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 531 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 83 optimal weight: 1.9990 chunk 112 optimal weight: 0.0970 chunk 96 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 147 optimal weight: 30.0000 chunk 1 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 425 ASN ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.187982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.123781 restraints weight = 17423.415| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.60 r_work: 0.3463 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3476 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10899 Z= 0.180 Angle : 0.570 10.152 14910 Z= 0.288 Chirality : 0.042 0.167 1725 Planarity : 0.004 0.074 1969 Dihedral : 4.332 30.905 1706 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.61 % Allowed : 15.91 % Favored : 82.47 % 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: 0.92 (0.22), residues: 1500 helix: 2.71 (0.20), residues: 666 sheet: -1.04 (0.44), residues: 131 loop : -1.21 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 3 59 TYR 0.012 0.001 TYR 3 256 PHE 0.017 0.001 PHE 2 327 TRP 0.011 0.001 TRP 2 349 HIS 0.004 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00427 (10880) covalent geometry : angle 0.56894 (14870) SS BOND : bond 0.00187 ( 17) SS BOND : angle 0.64299 ( 34) hydrogen bonds : bond 0.03277 ( 523) hydrogen bonds : angle 3.60101 ( 1536) link_NAG-ASN : bond 0.00263 ( 2) link_NAG-ASN : angle 1.54314 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3293.82 seconds wall clock time: 57 minutes 12.47 seconds (3432.47 seconds total)