Starting phenix.real_space_refine on Thu Jul 2 23:38:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jd1_36172/07_2026/8jd1_36172.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd1_36172/07_2026/8jd1_36172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jd1_36172/07_2026/8jd1_36172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd1_36172/07_2026/8jd1_36172.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jd1_36172/07_2026/8jd1_36172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd1_36172/07_2026/8jd1_36172.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jd1_36172/07_2026/8jd1_36172.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jd1_36172/07_2026/8jd1_36172.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.058 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 66 5.16 5 C 6876 2.51 5 N 1837 2.21 5 O 1987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10766 Number of models: 1 Model: "" Number of chains: 5 Chain: "2" Number of atoms: 5121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5121 Classifications: {'peptide': 750} Incomplete info: {'truncation_to_alanine': 193} Link IDs: {'PTRANS': 35, 'TRANS': 714} Chain breaks: 3 Unresolved non-hydrogen bonds: 767 Unresolved non-hydrogen angles: 982 Unresolved non-hydrogen dihedrals: 634 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLU:plan': 14, 'ASP:plan': 8, 'GLN:plan1': 9, 'ASN:plan1': 10, 'TYR:plan': 12, 'ARG:plan': 24, 'TRP:plan': 2, 'PHE:plan': 14, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 462 Chain: "3" Number of atoms: 5429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 756, 5429 Classifications: {'peptide': 756} Incomplete info: {'truncation_to_alanine': 151} Link IDs: {'PTRANS': 31, 'TRANS': 724} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 587 Unresolved non-hydrogen angles: 738 Unresolved non-hydrogen dihedrals: 497 Unresolved non-hydrogen chiralities: 49 Planarities with less than four sites: {'ARG:plan': 11, 'ASN:plan1': 9, 'GLU:plan': 9, 'ASP:plan': 9, 'GLN:plan1': 5, 'TYR:plan': 9, 'PHE:plan': 11, 'HIS:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 313 Chain: "2" 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: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "3" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 196 Unusual residues: {'CLR': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 2.58, per 1000 atoms: 0.24 Number of scatterers: 10766 At special positions: 0 Unit cell: (91.035, 114.597, 185.283, 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 66 16.00 O 1987 8.00 N 1837 7.00 C 6876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 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 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 573.4 milliseconds 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2838 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 8 sheets defined 50.0% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain '2' and resid 58 through 75 removed outlier: 3.615A pdb=" N ARG 2 74 " --> pdb=" O ASP 2 70 " (cutoff:3.500A) Processing helix chain '2' and resid 94 through 108 removed outlier: 4.190A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL 2 106 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA 2 108 " --> pdb=" O ASP 2 104 " (cutoff:3.500A) Processing helix chain '2' and resid 144 through 156 Processing helix chain '2' and resid 169 through 173 removed outlier: 3.855A pdb=" N LEU 2 172 " --> pdb=" O SER 2 169 " (cutoff:3.500A) Processing helix chain '2' and resid 190 through 202 removed outlier: 3.935A pdb=" N ALA 2 194 " --> pdb=" O PHE 2 190 " (cutoff:3.500A) Processing helix chain '2' and resid 214 through 229 removed outlier: 3.878A pdb=" N ARG 2 229 " --> pdb=" O GLU 2 225 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 258 removed outlier: 3.602A pdb=" N PHE 2 250 " --> pdb=" O SER 2 246 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU 2 251 " --> pdb=" O ARG 2 247 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY 2 252 " --> pdb=" O ALA 2 248 " (cutoff:3.500A) Processing helix chain '2' and resid 271 through 286 Processing helix chain '2' and resid 295 through 298 Processing helix chain '2' and resid 300 through 305 removed outlier: 3.911A pdb=" N VAL 2 304 " --> pdb=" O LEU 2 300 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 332 removed outlier: 3.687A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 344 through 354 Processing helix chain '2' and resid 356 through 360 Processing helix chain '2' and resid 377 through 400 removed outlier: 3.615A pdb=" N VAL 2 381 " --> pdb=" O LYS 2 377 " (cutoff:3.500A) Processing helix chain '2' and resid 407 through 411 Processing helix chain '2' and resid 414 through 423 removed outlier: 3.596A pdb=" N LYS 2 420 " --> pdb=" O ARG 2 416 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL 2 423 " --> pdb=" O TYR 2 419 " (cutoff:3.500A) Processing helix chain '2' and resid 481 through 485 Processing helix chain '2' and resid 568 through 593 removed outlier: 3.529A pdb=" N CYS 2 576 " --> pdb=" O VAL 2 572 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL 2 588 " --> pdb=" O PHE 2 584 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE 2 589 " --> pdb=" O VAL 2 585 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL 2 590 " --> pdb=" O LEU 2 586 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N HIS 2 592 " --> pdb=" O VAL 2 588 " (cutoff:3.500A) Processing helix chain '2' and resid 596 through 600 Processing helix chain '2' and resid 602 through 622 removed outlier: 3.826A pdb=" N PHE 2 621 " --> pdb=" O TYR 2 617 " (cutoff:3.500A) Processing helix chain '2' and resid 628 through 660 removed outlier: 3.705A pdb=" N THR 2 633 " --> pdb=" O THR 2 629 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG 2 636 " --> pdb=" O CYS 2 632 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU 2 639 " --> pdb=" O ARG 2 635 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER 2 644 " --> pdb=" O GLY 2 640 " (cutoff:3.500A) Processing helix chain '2' and resid 675 through 702 removed outlier: 4.378A pdb=" N VAL 2 680 " --> pdb=" O PRO 2 676 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N ALA 2 681 " --> pdb=" O ALA 2 677 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS 2 683 " --> pdb=" O GLN 2 679 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL 2 699 " --> pdb=" O VAL 2 695 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N VAL 2 700 " --> pdb=" O ALA 2 696 " (cutoff:3.500A) Processing helix chain '2' and resid 721 through 750 removed outlier: 3.604A pdb=" N ALA 2 726 " --> pdb=" O ASN 2 722 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU 2 729 " --> pdb=" O ASP 2 725 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY 2 730 " --> pdb=" O ALA 2 726 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU 2 738 " --> pdb=" O TYR 2 734 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ARG 2 750 " --> pdb=" O ALA 2 746 " (cutoff:3.500A) Processing helix chain '2' and resid 756 through 782 removed outlier: 3.984A pdb=" N LYS 2 760 " --> pdb=" O PHE 2 756 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU 2 777 " --> pdb=" O TRP 2 773 " (cutoff:3.500A) Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 788 through 810 removed outlier: 3.603A pdb=" N CYS 2 795 " --> pdb=" O THR 2 791 " (cutoff:3.500A) Processing helix chain '2' and resid 810 through 817 Processing helix chain '3' and resid 65 through 81 Processing helix chain '3' and resid 101 through 110 removed outlier: 3.594A pdb=" N GLU 3 107 " --> pdb=" O THR 3 103 " (cutoff:3.500A) Processing helix chain '3' and resid 111 through 115 removed outlier: 4.029A pdb=" N ALA 3 115 " --> pdb=" O PHE 3 112 " (cutoff:3.500A) Processing helix chain '3' and resid 150 through 165 removed outlier: 3.996A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE 3 164 " --> pdb=" O LEU 3 160 " (cutoff:3.500A) Processing helix chain '3' and resid 195 through 208 removed outlier: 3.513A pdb=" N LYS 3 199 " --> pdb=" O PHE 3 195 " (cutoff:3.500A) Processing helix chain '3' and resid 220 through 237 removed outlier: 3.868A pdb=" N GLU 3 224 " --> pdb=" O GLY 3 220 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR 3 225 " --> pdb=" O ASP 3 221 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY 3 226 " --> pdb=" O TYR 3 222 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA 3 229 " --> pdb=" O THR 3 225 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN 3 232 " --> pdb=" O GLU 3 228 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 3 233 " --> pdb=" O ALA 3 229 " (cutoff:3.500A) Processing helix chain '3' and resid 255 through 265 Processing helix chain '3' and resid 277 through 292 removed outlier: 3.751A pdb=" N ARG 3 282 " --> pdb=" O SER 3 278 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU 3 283 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU 3 284 " --> pdb=" O ASP 3 280 " (cutoff:3.500A) Processing helix chain '3' and resid 330 through 339 removed outlier: 3.796A pdb=" N ASP 3 334 " --> pdb=" O VAL 3 330 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR 3 336 " --> pdb=" O GLN 3 332 " (cutoff:3.500A) Processing helix chain '3' and resid 350 through 359 Processing helix chain '3' and resid 380 through 384 removed outlier: 3.828A pdb=" N TYR 3 384 " --> pdb=" O SER 3 381 " (cutoff:3.500A) Processing helix chain '3' and resid 387 through 389 No H-bonds generated for 'chain '3' and resid 387 through 389' Processing helix chain '3' and resid 390 through 412 removed outlier: 4.032A pdb=" N MET 3 400 " --> pdb=" O ALA 3 396 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR 3 410 " --> pdb=" O LYS 3 406 " (cutoff:3.500A) Processing helix chain '3' and resid 419 through 423 removed outlier: 3.521A pdb=" N LYS 3 423 " --> pdb=" O ASP 3 420 " (cutoff:3.500A) Processing helix chain '3' and resid 427 through 435 removed outlier: 3.548A pdb=" N ASP 3 433 " --> pdb=" O LYS 3 429 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR 3 434 " --> pdb=" O LEU 3 430 " (cutoff:3.500A) Processing helix chain '3' and resid 436 through 438 No H-bonds generated for 'chain '3' and resid 436 through 438' Processing helix chain '3' and resid 575 through 577 No H-bonds generated for 'chain '3' and resid 575 through 577' Processing helix chain '3' and resid 578 through 602 removed outlier: 3.601A pdb=" N THR 3 582 " --> pdb=" O ILE 3 578 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE 3 583 " --> pdb=" O GLY 3 579 " (cutoff:3.500A) Processing helix chain '3' and resid 613 through 633 removed outlier: 3.602A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) Processing helix chain '3' and resid 637 through 664 removed outlier: 3.833A pdb=" N ARG 3 645 " --> pdb=" O CYS 3 641 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU 3 646 " --> pdb=" O ALA 3 642 " (cutoff:3.500A) Processing helix chain '3' and resid 682 through 705 removed outlier: 3.809A pdb=" N SER 3 686 " --> pdb=" O PHE 3 682 " (cutoff:3.500A) Processing helix chain '3' and resid 707 through 711 Processing helix chain '3' and resid 733 through 754 removed outlier: 3.752A pdb=" N LEU 3 738 " --> pdb=" O ASP 3 734 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR 3 743 " --> pdb=" O ILE 3 739 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL 3 748 " --> pdb=" O ASP 3 744 " (cutoff:3.500A) Processing helix chain '3' and resid 761 through 792 removed outlier: 4.296A pdb=" N ASN 3 766 " --> pdb=" O PRO 3 762 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU 3 767 " --> pdb=" O GLU 3 763 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR 3 776 " --> pdb=" O GLY 3 772 " (cutoff:3.500A) Proline residue: 3 787 - end of helix Processing helix chain '3' and resid 799 through 829 removed outlier: 3.531A pdb=" N VAL 3 814 " --> pdb=" O SER 3 810 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU 3 815 " --> pdb=" O GLY 3 811 " (cutoff:3.500A) removed outlier: 3.751A 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 28 removed outlier: 3.730A pdb=" N ALA 2 86 " --> pdb=" O LEU 2 28 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL 2 139 " --> pdb=" O ILE 2 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 206 through 210 removed outlier: 7.646A pdb=" N VAL 2 207 " --> pdb=" O ALA 2 236 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER 2 238 " --> pdb=" O VAL 2 207 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N THR 2 209 " --> pdb=" O SER 2 238 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain '2' and resid 265 through 268 removed outlier: 3.633A pdb=" N LEU 2 268 " --> pdb=" O VAL 2 292 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 317 through 319 removed outlier: 6.266A pdb=" N TYR 2 453 " --> pdb=" O TYR 2 473 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N TYR 2 473 " --> pdb=" O TYR 2 453 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE 2 455 " --> pdb=" O VAL 2 471 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN 2 469 " --> pdb=" O THR 2 457 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '3' and resid 91 through 97 removed outlier: 3.566A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY 3 43 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE 3 45 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL 3 40 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL 3 145 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N GLY 3 42 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N ILE 3 169 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N VAL 3 145 " --> pdb=" O ILE 3 169 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLN 3 168 " --> pdb=" O ALA 3 188 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '3' and resid 240 through 244 removed outlier: 7.806A pdb=" N VAL 3 213 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ALA 3 244 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N THR 3 215 " --> pdb=" O ALA 3 244 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR 3 212 " --> pdb=" O VAL 3 271 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL 3 273 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER 3 214 " --> pdb=" O VAL 3 273 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N TYR 3 466 " --> pdb=" O HIS 3 485 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N HIS 3 485 " --> pdb=" O TYR 3 466 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL 3 468 " --> pdb=" O VAL 3 483 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '3' and resid 554 through 555 Processing sheet with id=AA8, first strand: chain '3' and resid 716 through 718 515 hydrogen bonds defined for protein. 1482 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3557 1.35 - 1.46: 2562 1.46 - 1.58: 4805 1.58 - 1.70: 0 1.70 - 1.82: 83 Bond restraints: 11007 Sorted by residual: bond pdb=" C ALA 2 811 " pdb=" N PRO 2 812 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.38e-02 5.25e+03 3.44e+00 bond pdb=" C GLU 21101 " pdb=" OXT GLU 21101 " ideal model delta sigma weight residual 1.231 1.256 -0.025 2.00e-02 2.50e+03 1.60e+00 bond pdb=" C GLU 21101 " pdb=" O GLU 21101 " ideal model delta sigma weight residual 1.231 1.255 -0.024 2.00e-02 2.50e+03 1.43e+00 bond pdb=" C3 CLR 31008 " pdb=" O1 CLR 31008 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" C3 CLR 31003 " pdb=" O1 CLR 31003 " ideal model delta sigma weight residual 1.413 1.434 -0.021 2.00e-02 2.50e+03 1.12e+00 ... (remaining 11002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 14608 1.16 - 2.32: 367 2.32 - 3.48: 79 3.48 - 4.64: 32 4.64 - 5.79: 11 Bond angle restraints: 15097 Sorted by residual: angle pdb=" CA VAL 3 483 " pdb=" C VAL 3 483 " pdb=" N GLY 3 484 " ideal model delta sigma weight residual 116.60 120.20 -3.60 1.45e+00 4.76e-01 6.15e+00 angle pdb=" C PRO 2 527 " pdb=" N TYR 2 528 " pdb=" CA TYR 2 528 " ideal model delta sigma weight residual 121.54 126.17 -4.63 1.91e+00 2.74e-01 5.89e+00 angle pdb=" C TYR 2 528 " pdb=" N GLU 2 529 " pdb=" CA GLU 2 529 " ideal model delta sigma weight residual 121.54 126.14 -4.60 1.91e+00 2.74e-01 5.79e+00 angle pdb=" C VAL 3 526 " pdb=" N CYS 3 527 " pdb=" CA CYS 3 527 " ideal model delta sigma weight residual 122.08 125.46 -3.38 1.47e+00 4.63e-01 5.28e+00 angle pdb=" CA GLN 3 829 " pdb=" C GLN 3 829 " pdb=" N PRO 3 830 " ideal model delta sigma weight residual 120.77 118.64 2.13 9.70e-01 1.06e+00 4.84e+00 ... (remaining 15092 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 5973 17.93 - 35.87: 400 35.87 - 53.80: 76 53.80 - 71.73: 12 71.73 - 89.66: 11 Dihedral angle restraints: 6472 sinusoidal: 2098 harmonic: 4374 Sorted by residual: dihedral pdb=" CB CYS 3 549 " pdb=" SG CYS 3 549 " pdb=" SG CYS 3 562 " pdb=" CB CYS 3 562 " ideal model delta sinusoidal sigma weight residual -86.00 -5.29 -80.71 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS 3 361 " pdb=" SG CYS 3 361 " pdb=" SG CYS 3 373 " pdb=" CB CYS 3 373 " ideal model delta sinusoidal sigma weight residual 93.00 22.14 70.86 1 1.00e+01 1.00e-02 6.45e+01 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 -132.58 46.58 1 1.00e+01 1.00e-02 3.00e+01 ... (remaining 6469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1044 0.028 - 0.056: 474 0.056 - 0.084: 176 0.084 - 0.111: 77 0.111 - 0.139: 18 Chirality restraints: 1789 Sorted by residual: chirality pdb=" CA ILE 2 485 " pdb=" N ILE 2 485 " pdb=" C ILE 2 485 " pdb=" CB ILE 2 485 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.84e-01 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 2.40 0.13 2.00e-01 2.50e+01 3.98e-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 2.39 0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 1786 not shown) Planarity restraints: 1931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU 2 556 " -0.042 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO 2 557 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO 2 557 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO 2 557 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA 2 811 " 0.040 5.00e-02 4.00e+02 6.12e-02 5.99e+00 pdb=" N PRO 2 812 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO 2 812 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO 2 812 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS 3 266 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO 3 267 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO 3 267 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO 3 267 " 0.019 5.00e-02 4.00e+02 ... (remaining 1928 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1841 2.76 - 3.30: 10871 3.30 - 3.83: 17169 3.83 - 4.37: 19194 4.37 - 4.90: 33041 Nonbonded interactions: 82116 Sorted by model distance: nonbonded pdb=" O TYR 3 626 " pdb=" OG1 THR 3 629 " model vdw 2.228 3.040 nonbonded pdb=" OH TYR 3 384 " pdb=" OE1 GLN 3 386 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR 3 792 " pdb=" O GLN 3 799 " model vdw 2.249 3.040 nonbonded pdb=" OG SER 3 327 " pdb=" O SER 3 388 " model vdw 2.254 3.040 nonbonded pdb=" OG SER 3 218 " pdb=" OD2 ASP 3 280 " model vdw 2.285 3.040 ... (remaining 82111 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.990 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.290 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 : 0.002 0.027 11024 Z= 0.103 Angle : 0.495 5.794 15131 Z= 0.248 Chirality : 0.039 0.139 1789 Planarity : 0.004 0.063 1931 Dihedral : 12.913 89.663 3583 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.21 % Allowed : 0.00 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.22), residues: 1488 helix: 1.38 (0.21), residues: 625 sheet: -1.90 (0.48), residues: 126 loop : -1.95 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 2 360 TYR 0.009 0.001 TYR 3 539 PHE 0.017 0.001 PHE 2 190 TRP 0.014 0.001 TRP 3 529 HIS 0.001 0.000 HIS 3 485 Details of bonding type rmsd/Z covalent geometry : bond 0.00208 / 0.10 (11007) covalent geometry : angle 0.49520 / 0.25 (15097) SS BOND : bond 0.00155 / 0.08 ( 17) SS BOND : angle 0.45927 / 0.32 ( 34) hydrogen bonds : bond 0.25127 / 17.70 ( 515) hydrogen bonds : angle 6.88562 / 5.11 ( 1482) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 0.382 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.0888 time to fit residues: 20.5355 Evaluate side-chains 115 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 1101 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 232 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.200137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.183944 restraints weight = 14417.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.180579 restraints weight = 22482.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.178935 restraints weight = 25035.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.178424 restraints weight = 23167.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.177412 restraints weight = 19872.783| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 11024 Z= 0.202 Angle : 0.602 9.332 15131 Z= 0.315 Chirality : 0.042 0.153 1789 Planarity : 0.004 0.049 1931 Dihedral : 5.307 86.192 1660 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.49 % Allowed : 8.29 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.22), residues: 1488 helix: 1.07 (0.20), residues: 657 sheet: -2.31 (0.44), residues: 142 loop : -1.97 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 2 156 TYR 0.018 0.002 TYR 3 222 PHE 0.021 0.002 PHE 2 250 TRP 0.016 0.001 TRP 2 697 HIS 0.003 0.001 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (11007) covalent geometry : angle 0.60177 / 0.31 (15097) SS BOND : bond 0.00491 / 0.38 ( 17) SS BOND : angle 0.62226 / 0.42 ( 34) hydrogen bonds : bond 0.06035 / 4.30 ( 515) hydrogen bonds : angle 4.84526 / 3.40 ( 1482) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.416 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 143 average time/residue: 0.0969 time to fit residues: 20.4398 Evaluate side-chains 114 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 78 LEU Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 2 residue 682 ILE Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 544 PHE Chi-restraints excluded: chain 3 residue 738 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 113 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.0980 chunk 115 optimal weight: 0.9980 chunk 60 optimal weight: 30.0000 chunk 121 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 97 HIS 2 414 ASN ** 2 469 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 = 0.4374 r_free = 0.4374 target = 0.199860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.184639 restraints weight = 14595.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.183131 restraints weight = 23900.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.181798 restraints weight = 27297.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.180280 restraints weight = 25528.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.179785 restraints weight = 27253.225| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11024 Z= 0.139 Angle : 0.562 10.479 15131 Z= 0.286 Chirality : 0.041 0.154 1789 Planarity : 0.004 0.050 1931 Dihedral : 5.140 86.423 1657 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.59 % Allowed : 13.07 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.22), residues: 1488 helix: 1.06 (0.20), residues: 655 sheet: -2.29 (0.44), residues: 142 loop : -1.89 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 57 TYR 0.016 0.001 TYR 3 256 PHE 0.021 0.001 PHE 2 250 TRP 0.011 0.001 TRP 3 529 HIS 0.002 0.001 HIS 2 97 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (11007) covalent geometry : angle 0.56206 / 0.29 (15097) SS BOND : bond 0.00219 / 0.14 ( 17) SS BOND : angle 0.60683 / 0.43 ( 34) hydrogen bonds : bond 0.04507 / 3.20 ( 515) hydrogen bonds : angle 4.45717 / 3.11 ( 1482) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.461 Fit side-chains revert: symmetry clash REVERT: 2 101 GLN cc_start: 0.7334 (mm-40) cc_final: 0.7122 (mm-40) REVERT: 3 275 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8161 (t80) REVERT: 3 645 ARG cc_start: 0.5576 (ttt180) cc_final: 0.5202 (ptm160) outliers start: 15 outliers final: 10 residues processed: 122 average time/residue: 0.0928 time to fit residues: 17.0218 Evaluate side-chains 111 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 201 PHE Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 446 PHE Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 140 LEU Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 544 PHE Chi-restraints excluded: chain 3 residue 646 LEU Chi-restraints excluded: chain 3 residue 738 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 93 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 chunk 111 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 469 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 = 0.4337 r_free = 0.4337 target = 0.196122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.180847 restraints weight = 14575.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.177764 restraints weight = 23734.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177013 restraints weight = 25777.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.176233 restraints weight = 23193.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.175676 restraints weight = 23192.847| |-----------------------------------------------------------------------------| r_work (final): 0.4130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11024 Z= 0.179 Angle : 0.594 8.810 15131 Z= 0.305 Chirality : 0.042 0.176 1789 Planarity : 0.004 0.057 1931 Dihedral : 5.251 86.450 1657 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 2.23 % Allowed : 15.09 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.22), residues: 1488 helix: 1.07 (0.20), residues: 669 sheet: -2.29 (0.45), residues: 135 loop : -1.98 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 3 723 TYR 0.022 0.002 TYR 2 386 PHE 0.017 0.002 PHE 2 250 TRP 0.037 0.002 TRP 2 567 HIS 0.003 0.001 HIS 3 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (11007) covalent geometry : angle 0.59388 / 0.30 (15097) SS BOND : bond 0.00230 / 0.12 ( 17) SS BOND : angle 0.64635 / 0.47 ( 34) hydrogen bonds : bond 0.04189 / 2.99 ( 515) hydrogen bonds : angle 4.34278 / 3.04 ( 1482) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 107 time to evaluate : 0.262 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7357 (mt) REVERT: 3 256 TYR cc_start: 0.7384 (m-80) cc_final: 0.6994 (m-10) REVERT: 3 275 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8255 (t80) REVERT: 3 645 ARG cc_start: 0.5669 (ttt180) cc_final: 0.5421 (ptm160) outliers start: 21 outliers final: 13 residues processed: 121 average time/residue: 0.0740 time to fit residues: 13.5645 Evaluate side-chains 118 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 544 PHE Chi-restraints excluded: chain 3 residue 738 LEU Chi-restraints excluded: chain 3 residue 802 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 10 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.0370 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 34 optimal weight: 0.0670 chunk 130 optimal weight: 0.7980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 469 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 = 0.4352 r_free = 0.4352 target = 0.197801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.182640 restraints weight = 14651.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.180694 restraints weight = 25396.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.179016 restraints weight = 27680.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.178037 restraints weight = 27044.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.177718 restraints weight = 27927.082| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11024 Z= 0.124 Angle : 0.554 10.843 15131 Z= 0.280 Chirality : 0.041 0.183 1789 Planarity : 0.004 0.054 1931 Dihedral : 5.077 77.673 1657 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.65 % Favored : 93.35 % Rotamer: Outliers : 2.13 % Allowed : 16.26 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.22), residues: 1488 helix: 1.23 (0.20), residues: 669 sheet: -2.18 (0.47), residues: 128 loop : -1.92 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 723 TYR 0.016 0.001 TYR 2 386 PHE 0.012 0.001 PHE 3 632 TRP 0.023 0.001 TRP 2 567 HIS 0.002 0.000 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (11007) covalent geometry : angle 0.55429 / 0.28 (15097) SS BOND : bond 0.00169 / 0.10 ( 17) SS BOND : angle 0.54314 / 0.37 ( 34) hydrogen bonds : bond 0.03796 / 2.72 ( 515) hydrogen bonds : angle 4.21258 / 2.94 ( 1482) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7396 (mt) REVERT: 2 388 MET cc_start: 0.8118 (tpp) cc_final: 0.7499 (tpt) REVERT: 3 256 TYR cc_start: 0.7336 (m-80) cc_final: 0.7105 (m-10) REVERT: 3 275 PHE cc_start: 0.8622 (OUTLIER) cc_final: 0.8179 (t80) REVERT: 3 645 ARG cc_start: 0.5662 (ttt180) cc_final: 0.5385 (ptm160) outliers start: 20 outliers final: 12 residues processed: 122 average time/residue: 0.0847 time to fit residues: 15.7575 Evaluate side-chains 116 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 446 PHE Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 592 HIS Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 802 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 34 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 46 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 chunk 69 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 120 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 3 168 GLN 3 197 GLN 3 357 GLN 3 402 HIS 3 467 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.187881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.170995 restraints weight = 14702.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.168517 restraints weight = 23907.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.167164 restraints weight = 25073.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.166265 restraints weight = 23873.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.165333 restraints weight = 21063.051| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.102 11024 Z= 0.393 Angle : 0.788 10.977 15131 Z= 0.410 Chirality : 0.050 0.322 1789 Planarity : 0.005 0.052 1931 Dihedral : 5.847 80.526 1657 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.08 % Allowed : 17.00 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.22), residues: 1488 helix: 0.89 (0.20), residues: 672 sheet: -2.82 (0.42), residues: 136 loop : -2.12 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 3 723 TYR 0.034 0.003 TYR 3 256 PHE 0.026 0.002 PHE 2 250 TRP 0.016 0.002 TRP 2 567 HIS 0.006 0.002 HIS 3 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.39 (11007) covalent geometry : angle 0.78771 / 0.41 (15097) SS BOND : bond 0.00399 / 0.25 ( 17) SS BOND : angle 0.91636 / 0.62 ( 34) hydrogen bonds : bond 0.04829 / 3.42 ( 515) hydrogen bonds : angle 4.68919 / 3.29 ( 1482) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 104 time to evaluate : 0.379 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7588 (mt) REVERT: 3 256 TYR cc_start: 0.7749 (m-80) cc_final: 0.7395 (m-80) REVERT: 3 275 PHE cc_start: 0.9024 (OUTLIER) cc_final: 0.8477 (t80) REVERT: 3 645 ARG cc_start: 0.5877 (ttt180) cc_final: 0.5576 (ptm160) outliers start: 29 outliers final: 20 residues processed: 123 average time/residue: 0.0923 time to fit residues: 17.0406 Evaluate side-chains 120 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 37 LEU Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 207 VAL Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 385 VAL Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 2 residue 682 ILE Chi-restraints excluded: chain 3 residue 91 LEU Chi-restraints excluded: chain 3 residue 145 VAL 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 272 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 798 VAL Chi-restraints excluded: chain 3 residue 802 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 21 optimal weight: 0.6980 chunk 120 optimal weight: 0.0270 chunk 2 optimal weight: 0.9990 chunk 111 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 43 optimal weight: 0.0060 chunk 65 optimal weight: 8.9990 chunk 135 optimal weight: 20.0000 chunk 83 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 197 GLN 3 386 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.194303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.179128 restraints weight = 14477.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.176994 restraints weight = 22361.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.175815 restraints weight = 25720.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.173721 restraints weight = 25442.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.172253 restraints weight = 29031.210| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11024 Z= 0.129 Angle : 0.600 13.816 15131 Z= 0.301 Chirality : 0.042 0.204 1789 Planarity : 0.004 0.051 1931 Dihedral : 5.363 71.327 1657 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.02 % Allowed : 18.60 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1488 helix: 1.15 (0.20), residues: 670 sheet: -2.28 (0.53), residues: 96 loop : -2.05 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 723 TYR 0.020 0.002 TYR 2 386 PHE 0.016 0.001 PHE 2 250 TRP 0.014 0.001 TRP 2 563 HIS 0.006 0.001 HIS 2 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (11007) covalent geometry : angle 0.59989 / 0.30 (15097) SS BOND : bond 0.00477 / 0.38 ( 17) SS BOND : angle 0.54226 / 0.37 ( 34) hydrogen bonds : bond 0.03762 / 2.72 ( 515) hydrogen bonds : angle 4.34511 / 3.04 ( 1482) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.400 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7522 (mt) REVERT: 2 202 PHE cc_start: 0.5758 (OUTLIER) cc_final: 0.5544 (m-10) REVERT: 2 388 MET cc_start: 0.8096 (tpp) cc_final: 0.7861 (tpt) REVERT: 3 256 TYR cc_start: 0.7416 (m-80) cc_final: 0.7087 (m-80) REVERT: 3 275 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8583 (t80) REVERT: 3 478 TYR cc_start: 0.5652 (m-10) cc_final: 0.5399 (m-10) REVERT: 3 645 ARG cc_start: 0.5667 (ttt180) cc_final: 0.5438 (ptm160) outliers start: 19 outliers final: 13 residues processed: 117 average time/residue: 0.0968 time to fit residues: 16.7698 Evaluate side-chains 116 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 78 LEU Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 202 PHE Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 446 PHE Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 91 LEU Chi-restraints excluded: chain 3 residue 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 798 VAL Chi-restraints excluded: chain 3 residue 802 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 54 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 19 optimal weight: 0.0570 chunk 104 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 592 HIS ** 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 = 0.4298 r_free = 0.4298 target = 0.192264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.174841 restraints weight = 14592.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.172280 restraints weight = 24098.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.171583 restraints weight = 30202.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.170470 restraints weight = 22413.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.170094 restraints weight = 28108.397| |-----------------------------------------------------------------------------| r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11024 Z= 0.198 Angle : 0.637 13.422 15131 Z= 0.319 Chirality : 0.043 0.233 1789 Planarity : 0.004 0.051 1931 Dihedral : 5.408 69.099 1657 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 1.81 % Allowed : 19.77 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.22), residues: 1488 helix: 1.18 (0.20), residues: 668 sheet: -2.85 (0.42), residues: 138 loop : -1.94 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 723 TYR 0.020 0.002 TYR 2 386 PHE 0.015 0.001 PHE 2 250 TRP 0.012 0.001 TRP 2 567 HIS 0.006 0.001 HIS 2 592 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (11007) covalent geometry : angle 0.63662 / 0.32 (15097) SS BOND : bond 0.00226 / 0.14 ( 17) SS BOND : angle 0.59650 / 0.43 ( 34) hydrogen bonds : bond 0.03842 / 2.76 ( 515) hydrogen bonds : angle 4.35308 / 3.04 ( 1482) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.428 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7543 (mt) REVERT: 2 202 PHE cc_start: 0.5871 (OUTLIER) cc_final: 0.5581 (m-10) REVERT: 3 256 TYR cc_start: 0.7550 (m-80) cc_final: 0.7184 (m-80) REVERT: 3 275 PHE cc_start: 0.8925 (OUTLIER) cc_final: 0.8550 (t80) outliers start: 17 outliers final: 13 residues processed: 118 average time/residue: 0.0924 time to fit residues: 16.4217 Evaluate side-chains 116 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 202 PHE Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 446 PHE Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 91 LEU Chi-restraints excluded: chain 3 residue 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 435 LEU Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 798 VAL Chi-restraints excluded: chain 3 residue 802 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 123 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 132 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 592 HIS ** 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 = 0.4302 r_free = 0.4302 target = 0.192795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.175616 restraints weight = 14483.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.170739 restraints weight = 24713.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.169818 restraints weight = 35624.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.169698 restraints weight = 28488.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.169235 restraints weight = 26428.705| |-----------------------------------------------------------------------------| r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6990 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11024 Z= 0.171 Angle : 0.619 14.955 15131 Z= 0.307 Chirality : 0.042 0.244 1789 Planarity : 0.004 0.051 1931 Dihedral : 5.332 63.960 1657 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.85 % Favored : 93.08 % Rotamer: Outliers : 2.13 % Allowed : 19.87 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.22), residues: 1488 helix: 1.23 (0.20), residues: 673 sheet: -2.66 (0.45), residues: 122 loop : -1.92 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 723 TYR 0.019 0.002 TYR 2 386 PHE 0.015 0.001 PHE 2 422 TRP 0.013 0.001 TRP 3 499 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (11007) covalent geometry : angle 0.61920 / 0.31 (15097) SS BOND : bond 0.00221 / 0.14 ( 17) SS BOND : angle 0.59110 / 0.42 ( 34) hydrogen bonds : bond 0.03674 / 2.65 ( 515) hydrogen bonds : angle 4.29926 / 3.01 ( 1482) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 106 time to evaluate : 0.346 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7461 (mt) REVERT: 3 256 TYR cc_start: 0.7491 (m-80) cc_final: 0.7202 (m-80) REVERT: 3 275 PHE cc_start: 0.8934 (OUTLIER) cc_final: 0.8559 (t80) REVERT: 3 478 TYR cc_start: 0.5614 (m-80) cc_final: 0.5412 (m-10) outliers start: 20 outliers final: 16 residues processed: 119 average time/residue: 0.0844 time to fit residues: 15.5169 Evaluate side-chains 117 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 78 LEU Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 446 PHE Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 629 THR Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 91 LEU Chi-restraints excluded: chain 3 residue 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 435 LEU Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 798 VAL Chi-restraints excluded: chain 3 residue 802 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 149 optimal weight: 0.0020 chunk 121 optimal weight: 0.0370 chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 140 optimal weight: 0.0970 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 0.0060 chunk 47 optimal weight: 9.9990 chunk 20 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 overall best weight: 0.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 592 HIS ** 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 = 0.4345 r_free = 0.4345 target = 0.197285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.181950 restraints weight = 14596.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.180629 restraints weight = 23344.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.179178 restraints weight = 21935.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.176792 restraints weight = 24471.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.176514 restraints weight = 28370.378| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 11024 Z= 0.109 Angle : 0.585 14.340 15131 Z= 0.288 Chirality : 0.041 0.280 1789 Planarity : 0.004 0.051 1931 Dihedral : 4.983 58.367 1657 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.65 % Favored : 93.28 % Rotamer: Outliers : 1.49 % Allowed : 20.94 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.23), residues: 1488 helix: 1.39 (0.20), residues: 676 sheet: -2.59 (0.46), residues: 125 loop : -1.82 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 68 TYR 0.016 0.001 TYR 2 386 PHE 0.012 0.001 PHE 2 250 TRP 0.012 0.001 TRP 2 567 HIS 0.001 0.000 HIS 3 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (11007) covalent geometry : angle 0.58517 / 0.29 (15097) SS BOND : bond 0.00188 / 0.12 ( 17) SS BOND : angle 0.51665 / 0.35 ( 34) hydrogen bonds : bond 0.03325 / 2.42 ( 515) hydrogen bonds : angle 4.14818 / 2.91 ( 1482) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7483 (mt) REVERT: 2 388 MET cc_start: 0.8158 (tpp) cc_final: 0.7953 (tpt) REVERT: 3 256 TYR cc_start: 0.7208 (m-80) cc_final: 0.6972 (m-80) REVERT: 3 275 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8562 (t80) REVERT: 3 478 TYR cc_start: 0.5471 (m-80) cc_final: 0.5255 (m-10) outliers start: 14 outliers final: 11 residues processed: 126 average time/residue: 0.0789 time to fit residues: 15.2051 Evaluate side-chains 119 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 446 PHE Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 629 THR Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 123 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 2 97 HIS ** 2 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 472 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 = 0.4322 r_free = 0.4322 target = 0.194915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.175870 restraints weight = 14557.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.174776 restraints weight = 22723.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.173978 restraints weight = 22502.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.172890 restraints weight = 21900.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.171944 restraints weight = 20991.260| |-----------------------------------------------------------------------------| r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11024 Z= 0.145 Angle : 0.600 14.614 15131 Z= 0.294 Chirality : 0.042 0.278 1789 Planarity : 0.004 0.051 1931 Dihedral : 5.018 58.404 1657 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.85 % Favored : 93.08 % Rotamer: Outliers : 1.59 % Allowed : 21.15 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.23), residues: 1488 helix: 1.42 (0.20), residues: 680 sheet: -2.61 (0.44), residues: 130 loop : -1.83 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 467 TYR 0.016 0.002 TYR 2 386 PHE 0.013 0.001 PHE 2 269 TRP 0.010 0.001 TRP 3 499 HIS 0.003 0.001 HIS 3 402 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (11007) covalent geometry : angle 0.60004 / 0.29 (15097) SS BOND : bond 0.00202 / 0.13 ( 17) SS BOND : angle 0.47936 / 0.34 ( 34) hydrogen bonds : bond 0.03415 / 2.47 ( 515) hydrogen bonds : angle 4.14567 / 2.91 ( 1482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1645.53 seconds wall clock time: 29 minutes 11.71 seconds (1751.71 seconds total)