Starting phenix.real_space_refine on Sat Nov 16 17:08:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/11_2024/8jd0_36171.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/11_2024/8jd0_36171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/11_2024/8jd0_36171.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/11_2024/8jd0_36171.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/11_2024/8jd0_36171.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd0_36171/11_2024/8jd0_36171.cif" } resolution = 3.3 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= 0.002 sd= 0.065 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: 5 Type Number sf(0) Gaussians S 68 5.16 5 C 7210 2.51 5 N 1927 2.21 5 O 2056 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 11264 Number of models: 1 Model: "" Number of chains: 5 Chain: "2" Number of atoms: 5377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 766, 5377 Classifications: {'peptide': 766} Incomplete info: {'truncation_to_alanine': 162} Link IDs: {'PTRANS': 37, 'TRANS': 728} Chain breaks: 2 Unresolved non-hydrogen bonds: 625 Unresolved non-hydrogen angles: 800 Unresolved non-hydrogen dihedrals: 515 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 2, 'TYR:plan': 8, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 15, 'GLU:plan': 12, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 364 Chain: "3" Number of atoms: 5567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 5567 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 30, 'TRANS': 734} Chain breaks: 2 Unresolved non-hydrogen bonds: 518 Unresolved non-hydrogen angles: 657 Unresolved non-hydrogen dihedrals: 438 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 9, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 7, 'PHE:plan': 9, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 277 Chain: "2" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 156 Unusual residues: {'CLR': 4, 'J9R': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "3" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 154 Unusual residues: {'CLR': 5, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.39, per 1000 atoms: 0.66 Number of scatterers: 11264 At special positions: 0 Unit cell: (85.68, 116.739, 184.212, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 68 16.00 F 3 9.00 O 2056 8.00 N 1927 7.00 C 7210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 240 " - pdb=" SG CYS 3 527 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG 21101 " - " ASN 2 203 " " NAG 31002 " - " ASN 3 209 " Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.7 seconds 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2876 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 10 sheets defined 49.7% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain '2' and resid 59 through 74 Processing helix chain '2' and resid 94 through 110 removed outlier: 3.823A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL 2 106 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER 2 109 " --> pdb=" O PHE 2 105 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU 2 110 " --> pdb=" O VAL 2 106 " (cutoff:3.500A) Processing helix chain '2' and resid 144 through 157 removed outlier: 3.573A pdb=" N ILE 2 149 " --> pdb=" O SER 2 145 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) Processing helix chain '2' and resid 170 through 174 Processing helix chain '2' and resid 187 through 189 No H-bonds generated for 'chain '2' and resid 187 through 189' Processing helix chain '2' and resid 190 through 202 removed outlier: 4.010A pdb=" N ALA 2 194 " --> pdb=" O PHE 2 190 " (cutoff:3.500A) Processing helix chain '2' and resid 214 through 231 removed outlier: 5.002A pdb=" N ALA 2 223 " --> pdb=" O THR 2 219 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LEU 2 226 " --> pdb=" O GLU 2 222 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 259 Processing helix chain '2' and resid 271 through 286 Processing helix chain '2' and resid 294 through 298 removed outlier: 3.989A pdb=" N GLY 2 298 " --> pdb=" O ASP 2 295 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 305 removed outlier: 4.095A pdb=" N VAL 2 304 " --> pdb=" O LEU 2 300 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA 2 305 " --> pdb=" O GLU 2 301 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 300 through 305' Processing helix chain '2' and resid 326 through 333 Processing helix chain '2' and resid 344 through 353 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 Processing helix chain '2' and resid 407 through 411 Processing helix chain '2' and resid 414 through 421 removed outlier: 3.627A pdb=" N LEU 2 418 " --> pdb=" O ASN 2 414 " (cutoff:3.500A) Processing helix chain '2' and resid 422 through 426 removed outlier: 3.743A pdb=" N VAL 2 426 " --> pdb=" O VAL 2 423 " (cutoff:3.500A) Processing helix chain '2' and resid 516 through 520 Processing helix chain '2' and resid 564 through 567 removed outlier: 3.515A pdb=" N TRP 2 567 " --> pdb=" O GLY 2 564 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 564 through 567' Processing helix chain '2' and resid 568 through 592 Processing helix chain '2' and resid 594 through 600 removed outlier: 4.512A pdb=" N VAL 2 598 " --> pdb=" O ALA 2 594 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS 2 599 " --> pdb=" O THR 2 595 " (cutoff:3.500A) Processing helix chain '2' and resid 602 through 623 Processing helix chain '2' and resid 628 through 661 removed outlier: 3.923A pdb=" N GLY 2 640 " --> pdb=" O ARG 2 636 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE 2 643 " --> pdb=" O LEU 2 639 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU 2 650 " --> pdb=" O CYS 2 646 " (cutoff:3.500A) Processing helix chain '2' and resid 678 through 700 Processing helix chain '2' and resid 724 through 748 removed outlier: 3.784A pdb=" N SER 2 731 " --> pdb=" O SER 2 727 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR 2 734 " --> pdb=" O GLY 2 730 " (cutoff:3.500A) Processing helix chain '2' and resid 755 through 783 removed outlier: 3.632A pdb=" N LYS 2 760 " --> pdb=" O PHE 2 756 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY 2 763 " --> pdb=" O ALA 2 759 " (cutoff:3.500A) Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 787 through 820 removed outlier: 4.120A 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 81 removed outlier: 3.710A pdb=" N LYS 3 81 " --> pdb=" O ASP 3 77 " (cutoff:3.500A) Processing helix chain '3' and resid 101 through 109 Processing helix chain '3' and resid 110 through 117 removed outlier: 3.516A pdb=" N ARG 3 114 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ALA 3 115 " --> pdb=" O PHE 3 112 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU 3 117 " --> pdb=" O ARG 3 114 " (cutoff:3.500A) Processing helix chain '3' and resid 150 through 165 removed outlier: 4.209A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE 3 164 " --> pdb=" O LEU 3 160 " (cutoff:3.500A) Processing helix chain '3' and resid 193 through 208 removed outlier: 4.164A pdb=" N GLN 3 197 " --> pdb=" O PRO 3 193 " (cutoff:3.500A) Processing helix chain '3' and resid 220 through 237 removed outlier: 4.128A pdb=" N THR 3 225 " --> pdb=" O ASP 3 221 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG 3 237 " --> pdb=" O GLU 3 233 " (cutoff:3.500A) Processing helix chain '3' and resid 254 through 265 Processing helix chain '3' and resid 277 through 291 removed outlier: 3.868A pdb=" N GLU 3 283 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) Processing helix chain '3' and resid 330 through 339 Processing helix chain '3' and resid 350 through 359 Processing helix chain '3' and resid 387 through 389 No H-bonds generated for 'chain '3' and resid 387 through 389' Processing helix chain '3' and resid 390 through 412 Processing helix chain '3' and resid 426 through 434 Processing helix chain '3' and resid 577 through 603 removed outlier: 3.576A pdb=" N VAL 3 581 " --> pdb=" O ALA 3 577 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N PHE 3 598 " --> pdb=" O VAL 3 594 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE 3 599 " --> pdb=" O VAL 3 595 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS 3 600 " --> pdb=" O THR 3 596 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N HIS 3 601 " --> pdb=" O VAL 3 597 " (cutoff:3.500A) Processing helix chain '3' and resid 611 through 634 removed outlier: 3.501A pdb=" N GLY 3 621 " --> pdb=" O ILE 3 617 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N PHE 3 631 " --> pdb=" O CYS 3 627 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE 3 632 " --> pdb=" O MET 3 628 " (cutoff:3.500A) Processing helix chain '3' and resid 637 through 664 removed outlier: 3.810A pdb=" N ALA 3 642 " --> pdb=" O PRO 3 638 " (cutoff:3.500A) Processing helix chain '3' and resid 682 through 702 removed outlier: 3.818A pdb=" N SER 3 686 " --> pdb=" O PHE 3 682 " (cutoff:3.500A) Processing helix chain '3' and resid 704 through 709 removed outlier: 4.061A pdb=" N LEU 3 709 " --> pdb=" O VAL 3 705 " (cutoff:3.500A) Processing helix chain '3' and resid 728 through 755 removed outlier: 4.135A pdb=" N ILE 3 739 " --> pdb=" O SER 3 735 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU 3 747 " --> pdb=" O TYR 3 743 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL 3 748 " --> pdb=" O ASP 3 744 " (cutoff:3.500A) Processing helix chain '3' and resid 761 through 763 No H-bonds generated for 'chain '3' and resid 761 through 763' Processing helix chain '3' and resid 764 through 791 removed outlier: 3.552A pdb=" N CYS 3 779 " --> pdb=" O MET 3 775 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE 3 780 " --> pdb=" O TYR 3 776 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU 3 786 " --> pdb=" O TRP 3 782 " (cutoff:3.500A) Proline residue: 3 787 - end of helix removed outlier: 3.732A pdb=" N TYR 3 790 " --> pdb=" O LEU 3 786 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N VAL 3 791 " --> pdb=" O PRO 3 787 " (cutoff:3.500A) Processing helix chain '3' and resid 798 through 804 Processing helix chain '3' and resid 804 through 819 Processing helix chain '3' and resid 819 through 828 removed outlier: 3.506A pdb=" N ILE 3 825 " --> pdb=" O PRO 3 821 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE 3 826 " --> pdb=" O LYS 3 822 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '2' and resid 84 through 90 removed outlier: 6.580A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N VAL 2 33 " --> pdb=" O ILE 2 136 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY 2 138 " --> pdb=" O VAL 2 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 162 through 164 removed outlier: 6.090A pdb=" N GLN 2 162 " --> pdb=" O ALA 2 182 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '2' and resid 234 through 240 removed outlier: 7.847A pdb=" N VAL 2 207 " --> pdb=" O ALA 2 236 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N SER 2 238 " --> pdb=" O VAL 2 207 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR 2 209 " --> pdb=" O SER 2 238 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N LYS 2 240 " --> pdb=" O THR 2 209 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA 2 211 " --> pdb=" O LYS 2 240 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N TYR 2 206 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL 2 267 " --> pdb=" O TYR 2 206 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER 2 208 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain '2' and resid 315 through 319 removed outlier: 6.507A pdb=" N TYR 2 453 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N TYR 2 473 " --> pdb=" O TYR 2 453 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE 2 455 " --> pdb=" O VAL 2 471 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG 2 467 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 33 through 34 removed outlier: 6.795A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL 3 40 " --> pdb=" O ILE 3 142 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY 3 144 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU 3 44 " --> pdb=" O ILE 3 146 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N ILE 3 169 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 6.560A 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 49 Processing sheet with id=AA7, first strand: chain '3' and resid 240 through 247 removed outlier: 7.646A pdb=" N VAL 3 213 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ALA 3 244 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N THR 3 215 " --> pdb=" O ALA 3 244 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS 3 246 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ALA 3 217 " --> pdb=" O LYS 3 246 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL 3 271 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER 3 214 " --> pdb=" O VAL 3 271 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL 3 216 " --> pdb=" O VAL 3 273 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE 3 275 " --> pdb=" O VAL 3 216 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TRP 3 297 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU 3 323 " --> pdb=" O TRP 3 297 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ALA 3 299 " --> pdb=" O LEU 3 323 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N LEU 3 325 " --> pdb=" O ALA 3 299 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N TYR 3 466 " --> pdb=" O HIS 3 485 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N HIS 3 485 " --> pdb=" O TYR 3 466 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL 3 468 " --> pdb=" O VAL 3 483 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL 3 474 " --> pdb=" O LYS 3 477 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 440 through 441 removed outlier: 3.689A pdb=" N PHE 3 440 " --> pdb=" O VAL 3 454 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 518 through 519 removed outlier: 3.635A pdb=" N ILE 3 532 " --> pdb=" O LYS 3 519 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 554 through 555 532 hydrogen bonds defined for protein. 1551 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: 3.61 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1838 1.31 - 1.44: 3046 1.44 - 1.56: 6559 1.56 - 1.69: 1 1.69 - 1.81: 86 Bond restraints: 11530 Sorted by residual: bond pdb=" C10 J9R 21102 " pdb=" N3 J9R 21102 " ideal model delta sigma weight residual 1.448 1.261 0.187 2.00e-02 2.50e+03 8.70e+01 bond pdb=" C6 J9R 21102 " pdb=" N1 J9R 21102 " ideal model delta sigma weight residual 1.335 1.451 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C15 J9R 21102 " pdb=" N3 J9R 21102 " ideal model delta sigma weight residual 1.458 1.380 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C2 J9R 21102 " pdb=" C3 J9R 21102 " ideal model delta sigma weight residual 1.459 1.526 -0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C11 J9R 21102 " pdb=" N3 J9R 21102 " ideal model delta sigma weight residual 1.448 1.385 0.063 2.00e-02 2.50e+03 1.01e+01 ... (remaining 11525 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 15627 2.01 - 4.03: 151 4.03 - 6.04: 20 6.04 - 8.05: 2 8.05 - 10.06: 2 Bond angle restraints: 15802 Sorted by residual: angle pdb=" C CYS 2 500 " pdb=" CA CYS 2 500 " pdb=" CB CYS 2 500 " ideal model delta sigma weight residual 117.23 111.22 6.01 1.36e+00 5.41e-01 1.95e+01 angle pdb=" CA CYS 2 500 " pdb=" C CYS 2 500 " pdb=" N SER 2 501 " ideal model delta sigma weight residual 119.98 117.14 2.84 8.50e-01 1.38e+00 1.11e+01 angle pdb=" CA PRO 3 139 " pdb=" N PRO 3 139 " pdb=" CD PRO 3 139 " ideal model delta sigma weight residual 112.00 107.38 4.62 1.40e+00 5.10e-01 1.09e+01 angle pdb=" CA LEU 2 639 " pdb=" CB LEU 2 639 " pdb=" CG LEU 2 639 " ideal model delta sigma weight residual 116.30 126.36 -10.06 3.50e+00 8.16e-02 8.27e+00 angle pdb=" C GLU 2 222 " pdb=" N ALA 2 223 " pdb=" CA ALA 2 223 " ideal model delta sigma weight residual 121.54 127.00 -5.46 1.91e+00 2.74e-01 8.17e+00 ... (remaining 15797 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.99: 6696 18.99 - 37.99: 503 37.99 - 56.98: 87 56.98 - 75.98: 18 75.98 - 94.97: 13 Dihedral angle restraints: 7317 sinusoidal: 2873 harmonic: 4444 Sorted by residual: dihedral pdb=" CB CYS 2 525 " pdb=" SG CYS 2 525 " pdb=" SG CYS 2 537 " pdb=" CB CYS 2 537 " ideal model delta sinusoidal sigma weight residual 93.00 178.71 -85.71 1 1.00e+01 1.00e-02 8.88e+01 dihedral pdb=" CB CYS 3 412 " pdb=" SG CYS 3 412 " pdb=" SG CYS 3 419 " pdb=" CB CYS 3 419 " ideal model delta sinusoidal sigma weight residual 93.00 168.75 -75.75 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS 2 632 " pdb=" SG CYS 2 632 " pdb=" SG CYS 2 721 " pdb=" CB CYS 2 721 " ideal model delta sinusoidal sigma weight residual 93.00 161.91 -68.91 1 1.00e+01 1.00e-02 6.15e+01 ... (remaining 7314 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1140 0.028 - 0.056: 457 0.056 - 0.084: 137 0.084 - 0.112: 95 0.112 - 0.140: 18 Chirality restraints: 1847 Sorted by residual: chirality pdb=" CA THR 2 595 " pdb=" N THR 2 595 " pdb=" C THR 2 595 " pdb=" CB THR 2 595 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA ILE 2 523 " pdb=" N ILE 2 523 " pdb=" C ILE 2 523 " pdb=" CB ILE 2 523 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.49e-01 chirality pdb=" CA SER 3 684 " pdb=" N SER 3 684 " pdb=" C SER 3 684 " pdb=" CB SER 3 684 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 1844 not shown) Planarity restraints: 2009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE 3 138 " -0.063 5.00e-02 4.00e+02 9.29e-02 1.38e+01 pdb=" N PRO 3 139 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO 3 139 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO 3 139 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA 2 223 " -0.012 2.00e-02 2.50e+03 2.47e-02 6.09e+00 pdb=" C ALA 2 223 " 0.043 2.00e-02 2.50e+03 pdb=" O ALA 2 223 " -0.016 2.00e-02 2.50e+03 pdb=" N PHE 2 224 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU 2 218 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C GLU 2 218 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU 2 218 " 0.011 2.00e-02 2.50e+03 pdb=" N THR 2 219 " 0.010 2.00e-02 2.50e+03 ... (remaining 2006 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2935 2.80 - 3.33: 10784 3.33 - 3.85: 18349 3.85 - 4.38: 20241 4.38 - 4.90: 35768 Nonbonded interactions: 88077 Sorted by model distance: nonbonded pdb=" O TYR 3 212 " pdb=" OG1 THR 3 506 " model vdw 2.278 3.040 nonbonded pdb=" OG SER 3 151 " pdb=" O GLU 31001 " model vdw 2.303 3.040 nonbonded pdb=" OG SER 3 149 " pdb=" OE1 GLU 31001 " model vdw 2.329 3.040 nonbonded pdb=" O GLY 3 579 " pdb=" OG1 THR 3 582 " model vdw 2.355 3.040 nonbonded pdb=" O ASP 2 421 " pdb=" ND2 ASN 2 425 " model vdw 2.361 3.120 ... (remaining 88072 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.380 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: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 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 : 0.004 0.187 11530 Z= 0.249 Angle : 0.488 10.063 15802 Z= 0.242 Chirality : 0.039 0.140 1847 Planarity : 0.003 0.093 2007 Dihedral : 13.565 94.974 4387 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.10 % Allowed : 12.94 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1519 helix: 1.86 (0.20), residues: 677 sheet: -1.35 (0.46), residues: 147 loop : -1.35 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 2 545 HIS 0.002 0.000 HIS 3 346 PHE 0.011 0.001 PHE 2 250 TYR 0.012 0.001 TYR 2 458 ARG 0.004 0.000 ARG 3 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 98 time to evaluate : 1.210 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.1993 time to fit residues: 30.7964 Evaluate side-chains 91 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 1001 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 39 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 138 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 735 ASN 3 168 GLN 3 345 ASN 3 369 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11530 Z= 0.383 Angle : 0.602 7.958 15802 Z= 0.312 Chirality : 0.044 0.167 1847 Planarity : 0.005 0.065 2007 Dihedral : 5.436 59.935 2288 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.49 % Allowed : 13.53 % Favored : 83.98 % 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: -0.17 (0.22), residues: 1519 helix: 1.47 (0.20), residues: 689 sheet: -1.60 (0.44), residues: 155 loop : -1.46 (0.23), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 2 545 HIS 0.003 0.001 HIS 3 402 PHE 0.020 0.002 PHE 3 598 TYR 0.024 0.002 TYR 3 212 ARG 0.006 0.001 ARG 3 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 1.295 Fit side-chains REVERT: 3 232 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7095 (mp10) REVERT: 3 276 MET cc_start: 0.8514 (ptm) cc_final: 0.7969 (ptm) REVERT: 3 453 ILE cc_start: 0.8943 (mm) cc_final: 0.8662 (mm) outliers start: 25 outliers final: 17 residues processed: 103 average time/residue: 0.1984 time to fit residues: 31.8720 Evaluate side-chains 101 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 399 LEU Chi-restraints excluded: chain 2 residue 501 SER Chi-restraints excluded: chain 2 residue 634 LEU Chi-restraints excluded: chain 2 residue 643 PHE Chi-restraints excluded: chain 2 residue 691 LEU Chi-restraints excluded: chain 2 residue 718 THR Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 345 ASN Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 499 TRP Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 646 LEU Chi-restraints excluded: chain 3 residue 824 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 93 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 47 optimal weight: 10.0000 chunk 110 optimal weight: 0.1980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11530 Z= 0.265 Angle : 0.524 8.026 15802 Z= 0.269 Chirality : 0.041 0.138 1847 Planarity : 0.004 0.057 2007 Dihedral : 5.061 61.624 2285 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.79 % Allowed : 14.53 % Favored : 82.69 % 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: -0.20 (0.22), residues: 1519 helix: 1.51 (0.20), residues: 690 sheet: -1.77 (0.42), residues: 155 loop : -1.50 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 2 545 HIS 0.003 0.001 HIS 3 402 PHE 0.015 0.001 PHE 2 67 TYR 0.019 0.001 TYR 3 212 ARG 0.004 0.000 ARG 3 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 1.104 Fit side-chains REVERT: 2 62 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8473 (tp) REVERT: 3 78 GLU cc_start: 0.6622 (mm-30) cc_final: 0.6403 (mm-30) REVERT: 3 276 MET cc_start: 0.8505 (ptm) cc_final: 0.8108 (ptm) REVERT: 3 453 ILE cc_start: 0.8957 (mm) cc_final: 0.8622 (mm) outliers start: 28 outliers final: 19 residues processed: 105 average time/residue: 0.1954 time to fit residues: 32.2468 Evaluate side-chains 103 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 83 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 634 LEU Chi-restraints excluded: chain 2 residue 643 PHE Chi-restraints excluded: chain 2 residue 691 LEU Chi-restraints excluded: chain 2 residue 718 THR Chi-restraints excluded: chain 3 residue 55 GLU Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 271 VAL Chi-restraints excluded: chain 3 residue 345 ASN Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 494 VAL Chi-restraints excluded: chain 3 residue 824 HIS Chi-restraints excluded: chain 3 residue 1001 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 71 optimal weight: 30.0000 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 chunk 146 optimal weight: 50.0000 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 365 HIS 2 469 GLN 3 345 ASN 3 369 HIS ** 3 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.108 11530 Z= 0.669 Angle : 0.734 10.103 15802 Z= 0.379 Chirality : 0.049 0.202 1847 Planarity : 0.005 0.063 2007 Dihedral : 5.916 63.352 2285 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.58 % Allowed : 15.42 % Favored : 81.00 % 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: -0.76 (0.21), residues: 1519 helix: 1.13 (0.20), residues: 686 sheet: -2.38 (0.42), residues: 150 loop : -1.80 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 2 349 HIS 0.004 0.001 HIS 3 402 PHE 0.027 0.002 PHE 2 67 TYR 0.028 0.003 TYR 3 212 ARG 0.007 0.001 ARG 3 183 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 1.232 Fit side-chains REVERT: 2 62 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8617 (tp) REVERT: 3 186 TYR cc_start: 0.8103 (m-80) cc_final: 0.7658 (m-80) REVERT: 3 232 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: 3 275 PHE cc_start: 0.8384 (OUTLIER) cc_final: 0.7374 (t80) REVERT: 3 276 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8192 (ptm) REVERT: 3 422 MET cc_start: 0.6674 (ttt) cc_final: 0.6414 (ttt) REVERT: 3 453 ILE cc_start: 0.8988 (mm) cc_final: 0.8633 (mm) REVERT: 3 463 MET cc_start: 0.7215 (ptp) cc_final: 0.6985 (ptp) outliers start: 36 outliers final: 28 residues processed: 108 average time/residue: 0.1927 time to fit residues: 32.8725 Evaluate side-chains 111 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 79 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 399 LEU Chi-restraints excluded: chain 2 residue 501 SER Chi-restraints excluded: chain 2 residue 634 LEU Chi-restraints excluded: chain 2 residue 643 PHE Chi-restraints excluded: chain 2 residue 651 LEU Chi-restraints excluded: chain 2 residue 691 LEU Chi-restraints excluded: chain 2 residue 718 THR Chi-restraints excluded: chain 3 residue 55 GLU Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 271 VAL Chi-restraints excluded: chain 3 residue 272 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 345 ASN Chi-restraints excluded: chain 3 residue 369 HIS Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 410 THR Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 646 LEU Chi-restraints excluded: chain 3 residue 824 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 4.9990 chunk 83 optimal weight: 0.3980 chunk 2 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 125 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 345 ASN ** 3 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11530 Z= 0.223 Angle : 0.535 10.941 15802 Z= 0.273 Chirality : 0.041 0.134 1847 Planarity : 0.004 0.065 2007 Dihedral : 5.569 63.577 2285 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.08 % Allowed : 16.62 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.22), residues: 1519 helix: 1.40 (0.20), residues: 688 sheet: -2.46 (0.41), residues: 146 loop : -1.72 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 2 545 HIS 0.008 0.001 HIS 3 369 PHE 0.024 0.001 PHE 2 250 TYR 0.015 0.001 TYR 3 212 ARG 0.003 0.000 ARG 3 370 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 86 time to evaluate : 1.206 Fit side-chains REVERT: 3 186 TYR cc_start: 0.7880 (m-80) cc_final: 0.7481 (m-80) REVERT: 3 232 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7090 (mp10) REVERT: 3 276 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8094 (ptm) REVERT: 3 453 ILE cc_start: 0.8961 (mm) cc_final: 0.8617 (mm) outliers start: 31 outliers final: 20 residues processed: 107 average time/residue: 0.1805 time to fit residues: 30.8373 Evaluate side-chains 104 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 634 LEU Chi-restraints excluded: chain 2 residue 643 PHE Chi-restraints excluded: chain 2 residue 651 LEU Chi-restraints excluded: chain 2 residue 691 LEU Chi-restraints excluded: chain 2 residue 718 THR Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 272 VAL Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 345 ASN Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 646 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 30.0000 chunk 132 optimal weight: 20.0000 chunk 29 optimal weight: 0.0980 chunk 86 optimal weight: 0.4980 chunk 36 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 122 optimal weight: 0.4980 chunk 68 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11530 Z= 0.216 Angle : 0.521 11.568 15802 Z= 0.264 Chirality : 0.040 0.134 1847 Planarity : 0.004 0.067 2007 Dihedral : 5.489 63.013 2285 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.08 % Allowed : 17.31 % Favored : 79.60 % 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: -0.42 (0.22), residues: 1519 helix: 1.51 (0.20), residues: 688 sheet: -2.44 (0.41), residues: 146 loop : -1.70 (0.22), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 2 545 HIS 0.003 0.001 HIS 3 485 PHE 0.019 0.001 PHE 2 250 TYR 0.015 0.001 TYR 3 212 ARG 0.005 0.000 ARG 3 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 1.420 Fit side-chains REVERT: 2 62 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8479 (tp) REVERT: 3 186 TYR cc_start: 0.7878 (m-80) cc_final: 0.7506 (m-80) REVERT: 3 232 GLN cc_start: 0.7798 (OUTLIER) cc_final: 0.7050 (mp10) REVERT: 3 275 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7263 (t80) REVERT: 3 276 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8106 (ptm) REVERT: 3 453 ILE cc_start: 0.8944 (mm) cc_final: 0.8604 (mm) outliers start: 31 outliers final: 19 residues processed: 109 average time/residue: 0.1787 time to fit residues: 31.0817 Evaluate side-chains 109 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 595 THR Chi-restraints excluded: chain 2 residue 634 LEU Chi-restraints excluded: chain 2 residue 643 PHE Chi-restraints excluded: chain 2 residue 718 THR Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 272 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 309 ILE Chi-restraints excluded: chain 3 residue 345 ASN Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 639 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 40.0000 chunk 16 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 123 optimal weight: 20.0000 chunk 82 optimal weight: 0.9990 chunk 146 optimal weight: 50.0000 chunk 91 optimal weight: 0.4980 chunk 89 optimal weight: 0.4980 chunk 67 optimal weight: 20.0000 chunk 90 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 41 HIS 3 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11530 Z= 0.203 Angle : 0.513 11.984 15802 Z= 0.259 Chirality : 0.040 0.134 1847 Planarity : 0.004 0.067 2007 Dihedral : 5.460 62.692 2285 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.79 % Allowed : 17.71 % Favored : 79.50 % 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: -0.33 (0.22), residues: 1519 helix: 1.59 (0.20), residues: 688 sheet: -2.40 (0.41), residues: 146 loop : -1.65 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 2 545 HIS 0.004 0.001 HIS 2 41 PHE 0.017 0.001 PHE 2 250 TYR 0.014 0.001 TYR 3 212 ARG 0.005 0.000 ARG 3 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 90 time to evaluate : 1.241 Fit side-chains REVERT: 3 36 GLU cc_start: 0.6712 (mp0) cc_final: 0.6459 (mp0) REVERT: 3 78 GLU cc_start: 0.6648 (mm-30) cc_final: 0.6425 (mm-30) REVERT: 3 186 TYR cc_start: 0.7840 (m-80) cc_final: 0.7537 (m-80) REVERT: 3 232 GLN cc_start: 0.7769 (OUTLIER) cc_final: 0.7061 (mp10) REVERT: 3 245 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7370 (mp0) REVERT: 3 275 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7205 (t80) REVERT: 3 276 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.8091 (ptm) REVERT: 3 453 ILE cc_start: 0.8951 (mm) cc_final: 0.8616 (mm) outliers start: 28 outliers final: 20 residues processed: 110 average time/residue: 0.2055 time to fit residues: 35.4932 Evaluate side-chains 111 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 595 THR Chi-restraints excluded: chain 2 residue 634 LEU Chi-restraints excluded: chain 2 residue 643 PHE Chi-restraints excluded: chain 2 residue 651 LEU Chi-restraints excluded: chain 2 residue 718 THR Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 245 GLU Chi-restraints excluded: chain 3 residue 272 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 309 ILE Chi-restraints excluded: chain 3 residue 345 ASN Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 646 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 9.9990 chunk 87 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 99 optimal weight: 0.1980 chunk 72 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 chunk 133 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11530 Z= 0.193 Angle : 0.509 12.147 15802 Z= 0.256 Chirality : 0.040 0.135 1847 Planarity : 0.004 0.067 2007 Dihedral : 5.455 62.352 2285 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.59 % Allowed : 18.01 % Favored : 79.40 % 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: -0.27 (0.22), residues: 1519 helix: 1.62 (0.20), residues: 687 sheet: -2.35 (0.41), residues: 146 loop : -1.61 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 2 545 HIS 0.003 0.001 HIS 3 402 PHE 0.015 0.001 PHE 2 250 TYR 0.014 0.001 TYR 3 212 ARG 0.005 0.000 ARG 3 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 1.169 Fit side-chains REVERT: 2 62 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8469 (tp) REVERT: 3 186 TYR cc_start: 0.7864 (m-80) cc_final: 0.7553 (m-80) REVERT: 3 232 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7032 (mp10) REVERT: 3 275 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7238 (t80) REVERT: 3 276 MET cc_start: 0.8358 (OUTLIER) cc_final: 0.8081 (ptm) REVERT: 3 453 ILE cc_start: 0.8910 (mm) cc_final: 0.8553 (mm) outliers start: 26 outliers final: 20 residues processed: 107 average time/residue: 0.1818 time to fit residues: 31.2430 Evaluate side-chains 110 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 595 THR Chi-restraints excluded: chain 2 residue 634 LEU Chi-restraints excluded: chain 2 residue 643 PHE Chi-restraints excluded: chain 2 residue 651 LEU Chi-restraints excluded: chain 2 residue 718 THR Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 272 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 309 ILE Chi-restraints excluded: chain 3 residue 345 ASN Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 646 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.3980 chunk 136 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 82 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 129 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 144 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11530 Z= 0.282 Angle : 0.543 12.115 15802 Z= 0.275 Chirality : 0.041 0.136 1847 Planarity : 0.004 0.067 2007 Dihedral : 5.541 62.260 2285 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.79 % Allowed : 17.71 % Favored : 79.50 % 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: -0.33 (0.22), residues: 1519 helix: 1.58 (0.20), residues: 688 sheet: -2.41 (0.42), residues: 146 loop : -1.63 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 2 545 HIS 0.003 0.001 HIS 3 402 PHE 0.017 0.001 PHE 3 74 TYR 0.021 0.001 TYR 3 434 ARG 0.005 0.000 ARG 3 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 1.131 Fit side-chains REVERT: 2 62 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8504 (tp) REVERT: 3 186 TYR cc_start: 0.7915 (m-80) cc_final: 0.7552 (m-80) REVERT: 3 232 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7054 (mp10) REVERT: 3 275 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7294 (t80) REVERT: 3 276 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8108 (ptm) REVERT: 3 453 ILE cc_start: 0.8941 (mm) cc_final: 0.8602 (mm) outliers start: 28 outliers final: 21 residues processed: 104 average time/residue: 0.1925 time to fit residues: 32.4224 Evaluate side-chains 111 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 595 THR Chi-restraints excluded: chain 2 residue 634 LEU Chi-restraints excluded: chain 2 residue 643 PHE Chi-restraints excluded: chain 2 residue 651 LEU Chi-restraints excluded: chain 2 residue 718 THR Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 272 VAL Chi-restraints excluded: chain 3 residue 273 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 309 ILE Chi-restraints excluded: chain 3 residue 345 ASN Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.3980 chunk 68 optimal weight: 9.9990 chunk 100 optimal weight: 0.2980 chunk 151 optimal weight: 6.9990 chunk 139 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 30.0000 chunk 95 optimal weight: 0.9980 chunk 128 optimal weight: 20.0000 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11530 Z= 0.203 Angle : 0.523 12.189 15802 Z= 0.263 Chirality : 0.040 0.135 1847 Planarity : 0.004 0.067 2007 Dihedral : 5.461 62.171 2285 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.49 % Allowed : 18.11 % Favored : 79.40 % 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: -0.27 (0.22), residues: 1519 helix: 1.64 (0.20), residues: 688 sheet: -2.39 (0.42), residues: 146 loop : -1.62 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 2 545 HIS 0.004 0.001 HIS 3 346 PHE 0.015 0.001 PHE 2 250 TYR 0.021 0.001 TYR 3 434 ARG 0.005 0.000 ARG 3 370 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3038 Ramachandran restraints generated. 1519 Oldfield, 0 Emsley, 1519 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.207 Fit side-chains REVERT: 2 62 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8479 (tp) REVERT: 3 186 TYR cc_start: 0.7881 (m-80) cc_final: 0.7571 (m-80) REVERT: 3 232 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: 3 275 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.7237 (t80) REVERT: 3 276 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.8092 (ptm) REVERT: 3 453 ILE cc_start: 0.8906 (mm) cc_final: 0.8555 (mm) outliers start: 25 outliers final: 20 residues processed: 101 average time/residue: 0.1830 time to fit residues: 29.7317 Evaluate side-chains 106 residues out of total 1302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 62 LEU Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 219 THR Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 595 THR Chi-restraints excluded: chain 2 residue 634 LEU Chi-restraints excluded: chain 2 residue 643 PHE Chi-restraints excluded: chain 2 residue 651 LEU Chi-restraints excluded: chain 2 residue 718 THR Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 216 VAL Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 272 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 309 ILE Chi-restraints excluded: chain 3 residue 345 ASN Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 474 VAL Chi-restraints excluded: chain 3 residue 481 LEU Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 646 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 120 optimal weight: 2.9990 chunk 50 optimal weight: 20.0000 chunk 124 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.200423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.169847 restraints weight = 13725.832| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.25 r_work: 0.3731 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11530 Z= 0.205 Angle : 0.519 12.214 15802 Z= 0.261 Chirality : 0.040 0.135 1847 Planarity : 0.004 0.067 2007 Dihedral : 5.441 61.971 2285 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.59 % Allowed : 18.01 % Favored : 79.40 % 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: -0.24 (0.22), residues: 1519 helix: 1.68 (0.20), residues: 687 sheet: -2.36 (0.42), residues: 146 loop : -1.62 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 2 545 HIS 0.004 0.001 HIS 3 346 PHE 0.015 0.001 PHE 2 250 TYR 0.024 0.001 TYR 3 434 ARG 0.005 0.000 ARG 3 370 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.05 seconds wall clock time: 41 minutes 57.63 seconds (2517.63 seconds total)