Starting phenix.real_space_refine on Tue May 13 19:58:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcv_36166/05_2025/8jcv_36166.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcv_36166/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jcv_36166/05_2025/8jcv_36166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcv_36166/05_2025/8jcv_36166.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcv_36166/05_2025/8jcv_36166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcv_36166/05_2025/8jcv_36166.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 7, 'HIS:plan': 1, 'TYR:plan': 10, 'ASN:plan1': 5, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 12, 'GLU:plan': 12, 'ARG:plan': 13} 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: {'GLN:plan1': 3, 'ASP:plan': 6, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 4, 'HIS:plan': 3, 'PHE:plan': 16, 'GLU:plan': 8, 'ARG:plan': 12} 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: 7.25, per 1000 atoms: 0.68 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: 2.40 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.42 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: 3.39 Time building geometry restraints manager: 2.87 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.000 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.970 ------------------------------------------------------------------------------- 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 : 7.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.015 0.001 TRP 3 554 HIS 0.005 0.000 HIS 2 390 PHE 0.010 0.001 PHE 2 250 TYR 0.010 0.001 TYR 3 478 ARG 0.010 0.000 ARG 2 74 Details of bonding type rmsd link_NAG-ASN : bond 0.00068 ( 2) link_NAG-ASN : angle 0.75579 ( 6) hydrogen bonds : bond 0.22306 ( 523) hydrogen bonds : angle 5.81387 ( 1536) SS BOND : bond 0.00179 ( 17) SS BOND : angle 0.99131 ( 34) covalent geometry : bond 0.00306 (10880) covalent geometry : angle 0.56105 (14870) *********************** 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 : 1.330 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: 0.2627 time to fit residues: 43.8595 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 : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 39 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 30.0000 chunk 118 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 chunk 88 optimal weight: 0.0770 chunk 137 optimal weight: 4.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- 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 3 405 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.192313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.136606 restraints weight = 16934.404| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 3.64 r_work: 0.3545 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10899 Z= 0.187 Angle : 0.583 11.148 14910 Z= 0.298 Chirality : 0.043 0.225 1725 Planarity : 0.004 0.064 1969 Dihedral : 5.042 38.316 1706 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.08 % Allowed : 7.53 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.22), residues: 1500 helix: 2.63 (0.20), residues: 652 sheet: -0.26 (0.45), residues: 138 loop : -1.11 (0.24), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 3 303 HIS 0.004 0.001 HIS 2 390 PHE 0.022 0.002 PHE 2 327 TYR 0.017 0.001 TYR 3 256 ARG 0.006 0.001 ARG 2 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00220 ( 2) link_NAG-ASN : angle 1.42433 ( 6) hydrogen bonds : bond 0.04751 ( 523) hydrogen bonds : angle 4.11799 ( 1536) SS BOND : bond 0.00209 ( 17) SS BOND : angle 1.29449 ( 34) covalent geometry : bond 0.00431 (10880) covalent geometry : angle 0.57935 (14870) *********************** 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 112 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 1.165 Fit side-chains REVERT: 2 238 SER cc_start: 0.8371 (t) cc_final: 0.8051 (p) REVERT: 2 245 MET cc_start: 0.4683 (OUTLIER) cc_final: 0.3767 (tmm) REVERT: 2 250 PHE cc_start: 0.6356 (m-10) cc_final: 0.6014 (m-10) REVERT: 2 410 MET cc_start: 0.7019 (ppp) cc_final: 0.6475 (ppp) REVERT: 3 49 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7044 (mt-10) outliers start: 10 outliers final: 6 residues processed: 107 average time/residue: 0.2392 time to fit residues: 36.4968 Evaluate side-chains 96 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 73 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 145 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.189991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.130465 restraints weight = 17171.968| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 3.58 r_work: 0.3517 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 10899 Z= 0.182 Angle : 0.552 9.350 14910 Z= 0.283 Chirality : 0.042 0.174 1725 Planarity : 0.004 0.062 1969 Dihedral : 4.817 32.580 1706 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.83 % Allowed : 10.32 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.22), residues: 1500 helix: 2.55 (0.20), residues: 658 sheet: -0.75 (0.42), residues: 138 loop : -1.14 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 3 303 HIS 0.004 0.001 HIS 2 390 PHE 0.019 0.001 PHE 2 327 TYR 0.015 0.001 TYR 2 216 ARG 0.006 0.001 ARG 2 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00312 ( 2) link_NAG-ASN : angle 1.60640 ( 6) hydrogen bonds : bond 0.04100 ( 523) hydrogen bonds : angle 3.87891 ( 1536) SS BOND : bond 0.00178 ( 17) SS BOND : angle 0.85363 ( 34) covalent geometry : bond 0.00426 (10880) covalent geometry : angle 0.55075 (14870) *********************** 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 110 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 1.181 Fit side-chains REVERT: 2 245 MET cc_start: 0.5201 (OUTLIER) cc_final: 0.4352 (tmm) REVERT: 2 334 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7673 (mp) REVERT: 2 410 MET cc_start: 0.6676 (ppp) cc_final: 0.6246 (ppp) REVERT: 3 49 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6836 (mt-10) REVERT: 3 239 ILE cc_start: 0.6783 (OUTLIER) cc_final: 0.6391 (mp) REVERT: 3 331 ARG cc_start: 0.8004 (mtt90) cc_final: 0.7469 (mmp-170) outliers start: 17 outliers final: 10 residues processed: 105 average time/residue: 0.2230 time to fit residues: 33.7779 Evaluate side-chains 97 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 72 optimal weight: 0.0770 chunk 33 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 = 0.4559 r_free = 0.4559 target = 0.191878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.137840 restraints weight = 17097.037| |-----------------------------------------------------------------------------| r_work (start): 0.3904 rms_B_bonded: 3.57 r_work: 0.3558 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3567 r_free = 0.3567 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10899 Z= 0.119 Angle : 0.504 7.111 14910 Z= 0.257 Chirality : 0.040 0.153 1725 Planarity : 0.003 0.066 1969 Dihedral : 4.471 27.063 1706 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.75 % Allowed : 13.01 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.22), residues: 1500 helix: 2.67 (0.20), residues: 655 sheet: -0.83 (0.42), residues: 138 loop : -1.20 (0.23), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP 2 337 HIS 0.003 0.000 HIS 2 390 PHE 0.011 0.001 PHE 2 327 TYR 0.023 0.001 TYR 2 216 ARG 0.003 0.000 ARG 2 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00067 ( 2) link_NAG-ASN : angle 1.36320 ( 6) hydrogen bonds : bond 0.03414 ( 523) hydrogen bonds : angle 3.65820 ( 1536) SS BOND : bond 0.00163 ( 17) SS BOND : angle 0.62416 ( 34) covalent geometry : bond 0.00272 (10880) covalent geometry : angle 0.50346 (14870) *********************** 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 98 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 1.231 Fit side-chains REVERT: 2 245 MET cc_start: 0.5441 (OUTLIER) cc_final: 0.4678 (tmm) REVERT: 2 334 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7577 (mp) REVERT: 2 410 MET cc_start: 0.6586 (ppp) cc_final: 0.6110 (ppp) REVERT: 3 72 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8168 (ttt) REVERT: 3 331 ARG cc_start: 0.7830 (mtt90) cc_final: 0.7358 (mmp-170) outliers start: 7 outliers final: 3 residues processed: 94 average time/residue: 0.2256 time to fit residues: 31.1700 Evaluate side-chains 88 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 3 residue 72 MET Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 565 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 78 optimal weight: 6.9990 chunk 134 optimal weight: 10.0000 chunk 90 optimal weight: 0.0870 chunk 135 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 130 optimal weight: 30.0000 chunk 59 optimal weight: 20.0000 chunk 3 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- 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 ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 402 HIS 3 731 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.184482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121553 restraints weight = 17128.465| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 3.37 r_work: 0.3365 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.093 10899 Z= 0.366 Angle : 0.717 13.185 14910 Z= 0.371 Chirality : 0.048 0.197 1725 Planarity : 0.005 0.068 1969 Dihedral : 5.345 39.435 1706 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.69 % Allowed : 13.55 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.22), residues: 1500 helix: 2.29 (0.20), residues: 664 sheet: -1.67 (0.40), residues: 148 loop : -1.37 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 3 303 HIS 0.007 0.001 HIS 2 87 PHE 0.023 0.003 PHE 2 327 TYR 0.014 0.002 TYR 3 256 ARG 0.008 0.001 ARG 2 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 2) link_NAG-ASN : angle 2.42836 ( 6) hydrogen bonds : bond 0.04458 ( 523) hydrogen bonds : angle 4.04575 ( 1536) SS BOND : bond 0.00260 ( 17) SS BOND : angle 0.71734 ( 34) covalent geometry : bond 0.00862 (10880) covalent geometry : angle 0.71533 (14870) *********************** 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 109 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.181 Fit side-chains REVERT: 2 245 MET cc_start: 0.5639 (OUTLIER) cc_final: 0.5040 (tmm) REVERT: 2 334 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7766 (mp) REVERT: 3 72 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.8346 (ttt) REVERT: 3 239 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6595 (mp) REVERT: 3 275 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.6811 (m-80) REVERT: 3 432 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7507 (ttmm) outliers start: 25 outliers final: 12 residues processed: 103 average time/residue: 0.2242 time to fit residues: 33.7202 Evaluate side-chains 95 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 198 ILE 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 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 227 ILE Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 275 PHE 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 432 LYS 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 65 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 139 optimal weight: 0.9980 chunk 118 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 162 GLN ** 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 = 0.4519 r_free = 0.4519 target = 0.187964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.129724 restraints weight = 17140.020| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 3.70 r_work: 0.3442 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10899 Z= 0.144 Angle : 0.551 9.612 14910 Z= 0.280 Chirality : 0.041 0.152 1725 Planarity : 0.004 0.073 1969 Dihedral : 4.759 37.290 1706 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.94 % Allowed : 15.27 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1500 helix: 2.39 (0.19), residues: 666 sheet: -1.56 (0.40), residues: 138 loop : -1.33 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 3 355 HIS 0.005 0.001 HIS 2 390 PHE 0.014 0.001 PHE 2 327 TYR 0.015 0.001 TYR 2 216 ARG 0.003 0.000 ARG 2 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00092 ( 2) link_NAG-ASN : angle 1.64211 ( 6) hydrogen bonds : bond 0.03528 ( 523) hydrogen bonds : angle 3.79052 ( 1536) SS BOND : bond 0.00259 ( 17) SS BOND : angle 1.11630 ( 34) covalent geometry : bond 0.00338 (10880) covalent geometry : angle 0.54769 (14870) *********************** 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 103 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 85 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5654 (OUTLIER) cc_final: 0.5004 (tmm) REVERT: 2 334 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7628 (mp) REVERT: 3 239 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6460 (mp) outliers start: 18 outliers final: 8 residues processed: 98 average time/residue: 0.2205 time to fit residues: 31.6429 Evaluate side-chains 92 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 258 LEU Chi-restraints excluded: chain 2 residue 334 LEU Chi-restraints excluded: chain 2 residue 413 VAL Chi-restraints excluded: chain 3 residue 89 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 84 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 94 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 58 optimal weight: 20.0000 chunk 110 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 94 HIS ** 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 = 0.4505 r_free = 0.4505 target = 0.186460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.125291 restraints weight = 17307.161| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 3.45 r_work: 0.3420 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 10899 Z= 0.198 Angle : 0.583 10.099 14910 Z= 0.297 Chirality : 0.042 0.168 1725 Planarity : 0.004 0.075 1969 Dihedral : 4.834 40.997 1706 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.26 % Allowed : 15.16 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.22), residues: 1500 helix: 2.40 (0.20), residues: 670 sheet: -1.52 (0.42), residues: 135 loop : -1.38 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP 2 297 HIS 0.004 0.001 HIS 2 390 PHE 0.020 0.002 PHE 2 327 TYR 0.013 0.002 TYR 3 256 ARG 0.005 0.000 ARG 2 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00300 ( 2) link_NAG-ASN : angle 1.72153 ( 6) hydrogen bonds : bond 0.03636 ( 523) hydrogen bonds : angle 3.80492 ( 1536) SS BOND : bond 0.00174 ( 17) SS BOND : angle 0.77677 ( 34) covalent geometry : bond 0.00470 (10880) covalent geometry : angle 0.58184 (14870) *********************** 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 102 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 1.092 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5318 (OUTLIER) cc_final: 0.4844 (tmm) REVERT: 2 334 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7669 (mp) REVERT: 3 72 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8396 (ttt) REVERT: 3 186 TYR cc_start: 0.8550 (m-10) cc_final: 0.8206 (m-10) REVERT: 3 239 ILE cc_start: 0.6830 (OUTLIER) cc_final: 0.6398 (mp) outliers start: 21 outliers final: 12 residues processed: 98 average time/residue: 0.2115 time to fit residues: 30.9068 Evaluate side-chains 95 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 221 ILE 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 89 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 292 ASN Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 492 LEU Chi-restraints excluded: chain 3 residue 531 CYS Chi-restraints excluded: chain 3 residue 565 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 10 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 143 optimal weight: 0.9990 chunk 138 optimal weight: 10.0000 chunk 122 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 chunk 117 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.187311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.131434 restraints weight = 17125.799| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 3.61 r_work: 0.3414 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3420 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3561 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= 0.158 Angle : 0.559 8.475 14910 Z= 0.283 Chirality : 0.041 0.154 1725 Planarity : 0.004 0.077 1969 Dihedral : 4.685 41.235 1706 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.94 % Allowed : 16.02 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.22), residues: 1500 helix: 2.50 (0.19), residues: 670 sheet: -1.57 (0.41), residues: 141 loop : -1.37 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 2 291 HIS 0.003 0.001 HIS 2 390 PHE 0.014 0.001 PHE 2 327 TYR 0.024 0.001 TYR 2 216 ARG 0.004 0.000 ARG 2 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00147 ( 2) link_NAG-ASN : angle 1.51113 ( 6) hydrogen bonds : bond 0.03372 ( 523) hydrogen bonds : angle 3.73666 ( 1536) SS BOND : bond 0.00303 ( 17) SS BOND : angle 0.84626 ( 34) covalent geometry : bond 0.00374 (10880) covalent geometry : angle 0.55792 (14870) *********************** 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 101 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.133 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5641 (OUTLIER) cc_final: 0.4957 (tmm) REVERT: 2 334 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7635 (mp) REVERT: 3 38 ASP cc_start: 0.7136 (m-30) cc_final: 0.6706 (t70) REVERT: 3 72 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8296 (ttt) REVERT: 3 186 TYR cc_start: 0.8525 (m-10) cc_final: 0.8103 (m-10) REVERT: 3 239 ILE cc_start: 0.6762 (OUTLIER) cc_final: 0.6487 (mp) outliers start: 18 outliers final: 11 residues processed: 98 average time/residue: 0.2269 time to fit residues: 32.7779 Evaluate side-chains 93 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 258 LEU 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 89 VAL Chi-restraints excluded: chain 3 residue 239 ILE Chi-restraints excluded: chain 3 residue 263 LEU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 492 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 58 optimal weight: 20.0000 chunk 141 optimal weight: 7.9990 chunk 71 optimal weight: 30.0000 chunk 9 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 259 GLN 2 723 HIS ** 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 = 0.4464 r_free = 0.4464 target = 0.182643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.122333 restraints weight = 17327.557| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.75 r_work: 0.3321 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.098 10899 Z= 0.336 Angle : 0.709 13.063 14910 Z= 0.363 Chirality : 0.047 0.177 1725 Planarity : 0.005 0.079 1969 Dihedral : 5.339 49.713 1706 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 2.26 % Allowed : 16.34 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1500 helix: 2.24 (0.20), residues: 671 sheet: -2.04 (0.40), residues: 149 loop : -1.48 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 3 355 HIS 0.006 0.001 HIS 2 87 PHE 0.022 0.002 PHE 2 327 TYR 0.024 0.002 TYR 2 216 ARG 0.007 0.001 ARG 2 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 2) link_NAG-ASN : angle 2.22184 ( 6) hydrogen bonds : bond 0.04094 ( 523) hydrogen bonds : angle 4.00880 ( 1536) SS BOND : bond 0.00372 ( 17) SS BOND : angle 0.89378 ( 34) covalent geometry : bond 0.00803 (10880) covalent geometry : angle 0.70686 (14870) *********************** 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 103 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 82 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5187 (OUTLIER) cc_final: 0.4824 (tmm) REVERT: 2 334 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7664 (mp) REVERT: 3 72 MET cc_start: 0.8766 (OUTLIER) cc_final: 0.8471 (ttt) REVERT: 3 239 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6464 (mp) outliers start: 21 outliers final: 14 residues processed: 97 average time/residue: 0.2174 time to fit residues: 31.3291 Evaluate side-chains 97 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 195 MET Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 258 LEU 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 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 275 PHE Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 388 SER Chi-restraints excluded: chain 3 residue 434 TYR Chi-restraints excluded: chain 3 residue 492 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 89 optimal weight: 0.6980 chunk 63 optimal weight: 9.9990 chunk 47 optimal weight: 0.6980 chunk 57 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 149 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 87 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: ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.186638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.129703 restraints weight = 17210.674| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 4.02 r_work: 0.3413 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3417 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10899 Z= 0.140 Angle : 0.576 8.732 14910 Z= 0.288 Chirality : 0.042 0.152 1725 Planarity : 0.004 0.079 1969 Dihedral : 4.845 47.274 1706 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.61 % Allowed : 16.99 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.22), residues: 1500 helix: 2.40 (0.20), residues: 672 sheet: -1.64 (0.41), residues: 145 loop : -1.42 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 349 HIS 0.003 0.001 HIS 2 390 PHE 0.013 0.001 PHE 2 327 TYR 0.022 0.001 TYR 2 216 ARG 0.004 0.000 ARG 2 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00103 ( 2) link_NAG-ASN : angle 1.52852 ( 6) hydrogen bonds : bond 0.03363 ( 523) hydrogen bonds : angle 3.77634 ( 1536) SS BOND : bond 0.00225 ( 17) SS BOND : angle 0.78466 ( 34) covalent geometry : bond 0.00327 (10880) covalent geometry : angle 0.57431 (14870) ********************** 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 99 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: 2 245 MET cc_start: 0.5667 (OUTLIER) cc_final: 0.5272 (tmm) REVERT: 2 334 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7653 (mp) REVERT: 2 410 MET cc_start: 0.6356 (ppp) cc_final: 0.6082 (ptt) REVERT: 3 38 ASP cc_start: 0.7106 (m-30) cc_final: 0.6660 (t70) REVERT: 3 49 GLU cc_start: 0.6795 (mt-10) cc_final: 0.6551 (mt-10) REVERT: 3 72 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8289 (ttt) REVERT: 3 186 TYR cc_start: 0.8567 (m-10) cc_final: 0.8168 (m-10) REVERT: 3 239 ILE cc_start: 0.6694 (OUTLIER) cc_final: 0.6298 (mp) outliers start: 15 outliers final: 11 residues processed: 96 average time/residue: 0.2332 time to fit residues: 32.5803 Evaluate side-chains 93 residues out of total 1284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 137 THR Chi-restraints excluded: chain 2 residue 221 ILE 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 72 MET 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 275 PHE Chi-restraints excluded: chain 3 residue 340 LEU Chi-restraints excluded: chain 3 residue 492 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 56 optimal weight: 20.0000 chunk 65 optimal weight: 0.0030 chunk 107 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 5 optimal weight: 0.0020 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.187670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.125493 restraints weight = 17192.424| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.48 r_work: 0.3483 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3492 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3492 r_free = 0.3492 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3492 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3913 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= 0.122 Angle : 0.559 8.259 14910 Z= 0.279 Chirality : 0.041 0.142 1725 Planarity : 0.004 0.076 1969 Dihedral : 4.648 45.310 1706 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 1.51 % Allowed : 17.42 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.22), residues: 1500 helix: 2.61 (0.20), residues: 666 sheet: -1.73 (0.41), residues: 145 loop : -1.42 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 349 HIS 0.003 0.000 HIS 2 390 PHE 0.012 0.001 PHE 2 422 TYR 0.026 0.001 TYR 2 216 ARG 0.004 0.000 ARG 3 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00080 ( 2) link_NAG-ASN : angle 1.32696 ( 6) hydrogen bonds : bond 0.03134 ( 523) hydrogen bonds : angle 3.67521 ( 1536) SS BOND : bond 0.00223 ( 17) SS BOND : angle 0.74941 ( 34) covalent geometry : bond 0.00283 (10880) covalent geometry : angle 0.55819 (14870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6174.72 seconds wall clock time: 107 minutes 11.98 seconds (6431.98 seconds total)