Starting phenix.real_space_refine on Sat Oct 11 02:33:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd1_36172/10_2025/8jd1_36172.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd1_36172/10_2025/8jd1_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jd1_36172/10_2025/8jd1_36172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd1_36172/10_2025/8jd1_36172.map" model { file = "/net/cci-nas-00/data/ceres_data/8jd1_36172/10_2025/8jd1_36172.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd1_36172/10_2025/8jd1_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-2.0-5842/lib/python3.9/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: 2.41, per 1000 atoms: 0.22 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: 0.79 Conformation dependent library (CDL) restraints added in 537.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.26 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: 1.75 Time building geometry restraints manager: 1.05 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: 6339 17.93 - 35.87: 418 35.87 - 53.80: 80 53.80 - 71.73: 16 71.73 - 89.66: 11 Dihedral angle restraints: 6864 sinusoidal: 2490 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 6861 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: 4.150 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: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.320 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 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 : 12.603 89.663 3975 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 aren 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 covalent geometry : bond 0.00208 (11007) covalent geometry : angle 0.49520 (15097) SS BOND : bond 0.00155 ( 17) SS BOND : angle 0.45927 ( 34) hydrogen bonds : bond 0.25127 ( 515) hydrogen bonds : angle 6.88562 ( 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 : 0.401 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.0877 time to fit residues: 20.1920 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 : 0.287 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4374 r_free = 0.4374 target = 0.199889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.183713 restraints weight = 14419.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.178822 restraints weight = 22748.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.177570 restraints weight = 27549.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.177347 restraints weight = 25240.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.176722 restraints weight = 19805.088| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 11024 Z= 0.206 Angle : 0.609 9.401 15131 Z= 0.319 Chirality : 0.042 0.158 1789 Planarity : 0.004 0.047 1931 Dihedral : 6.183 85.889 2052 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 1.59 % Allowed : 8.08 % Favored : 90.33 % 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 aren not related in a simple way. whole: -0.94 (0.22), residues: 1488 helix: 1.06 (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 0.005 0.001 ARG 2 156 TYR 0.019 0.002 TYR 3 222 PHE 0.019 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 covalent geometry : bond 0.00473 (11007) covalent geometry : angle 0.60851 (15097) SS BOND : bond 0.00244 ( 17) SS BOND : angle 0.61296 ( 34) hydrogen bonds : bond 0.05734 ( 515) hydrogen bonds : angle 4.82587 ( 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 149 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 134 time to evaluate : 0.394 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 144 average time/residue: 0.0958 time to fit residues: 20.1310 Evaluate side-chains 118 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 140 LEU 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: 0.6980 chunk 56 optimal weight: 2.9990 chunk 113 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 60 optimal weight: 20.0000 chunk 121 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 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 = 0.4366 r_free = 0.4366 target = 0.199006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.183387 restraints weight = 14547.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.181924 restraints weight = 25906.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.181159 restraints weight = 26818.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.179937 restraints weight = 23814.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.179924 restraints weight = 20734.847| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11024 Z= 0.151 Angle : 0.567 9.308 15131 Z= 0.290 Chirality : 0.041 0.153 1789 Planarity : 0.004 0.048 1931 Dihedral : 6.035 88.677 2049 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 1.70 % Allowed : 12.96 % 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 aren not related in a simple way. whole: -0.91 (0.22), residues: 1488 helix: 1.05 (0.20), residues: 654 sheet: -2.32 (0.44), residues: 142 loop : -1.90 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 57 TYR 0.016 0.002 TYR 3 256 PHE 0.020 0.001 PHE 2 250 TRP 0.011 0.001 TRP 3 529 HIS 0.003 0.001 HIS 2 77 Details of bonding type rmsd covalent geometry : bond 0.00346 (11007) covalent geometry : angle 0.56722 (15097) SS BOND : bond 0.00198 ( 17) SS BOND : angle 0.59471 ( 34) hydrogen bonds : bond 0.04597 ( 515) hydrogen bonds : angle 4.49481 ( 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 128 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: 2 101 GLN cc_start: 0.7346 (mm-40) cc_final: 0.7136 (mm-40) REVERT: 3 275 PHE cc_start: 0.8467 (OUTLIER) cc_final: 0.8139 (t80) REVERT: 3 645 ARG cc_start: 0.5464 (ttt180) cc_final: 0.5153 (ptm160) outliers start: 16 outliers final: 10 residues processed: 120 average time/residue: 0.0921 time to fit residues: 16.5432 Evaluate side-chains 112 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 294 SER 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: 4.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 89 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 97 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.196149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.178892 restraints weight = 14577.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.174918 restraints weight = 22471.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.174254 restraints weight = 28709.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.173616 restraints weight = 21605.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.172991 restraints weight = 21258.748| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11024 Z= 0.180 Angle : 0.589 9.149 15131 Z= 0.303 Chirality : 0.042 0.171 1789 Planarity : 0.004 0.055 1931 Dihedral : 6.028 81.853 2049 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 2.34 % Allowed : 14.77 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.22), residues: 1488 helix: 1.05 (0.20), residues: 665 sheet: -2.30 (0.45), residues: 135 loop : -2.00 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 723 TYR 0.020 0.002 TYR 2 386 PHE 0.016 0.001 PHE 2 250 TRP 0.040 0.002 TRP 2 567 HIS 0.003 0.001 HIS 3 498 Details of bonding type rmsd covalent geometry : bond 0.00426 (11007) covalent geometry : angle 0.58923 (15097) SS BOND : bond 0.00228 ( 17) SS BOND : angle 0.64870 ( 34) hydrogen bonds : bond 0.04228 ( 515) hydrogen bonds : angle 4.38727 ( 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 130 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.302 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7344 (mt) REVERT: 3 256 TYR cc_start: 0.7374 (m-80) cc_final: 0.6992 (m-10) REVERT: 3 275 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.8281 (t80) REVERT: 3 645 ARG cc_start: 0.5706 (ttt180) cc_final: 0.5440 (ptm160) outliers start: 22 outliers final: 15 residues processed: 121 average time/residue: 0.0887 time to fit residues: 16.1274 Evaluate side-chains 118 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 446 PHE Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 485 ILE 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: 0.7980 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 61 optimal weight: 7.9990 chunk 138 optimal weight: 0.9990 chunk 117 optimal weight: 2.9990 chunk 136 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.195138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.177492 restraints weight = 14374.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.176737 restraints weight = 23074.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.175348 restraints weight = 22778.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.173561 restraints weight = 25380.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.173083 restraints weight = 26207.935| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11024 Z= 0.168 Angle : 0.585 9.959 15131 Z= 0.297 Chirality : 0.042 0.163 1789 Planarity : 0.004 0.053 1931 Dihedral : 5.995 80.583 2049 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 2.87 % Allowed : 16.26 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.22), residues: 1488 helix: 1.16 (0.20), residues: 671 sheet: -2.32 (0.47), residues: 128 loop : -1.98 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 3 723 TYR 0.021 0.002 TYR 2 386 PHE 0.012 0.001 PHE 3 632 TRP 0.023 0.001 TRP 2 567 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00396 (11007) covalent geometry : angle 0.58528 (15097) SS BOND : bond 0.00194 ( 17) SS BOND : angle 0.58992 ( 34) hydrogen bonds : bond 0.03960 ( 515) hydrogen bonds : angle 4.29145 ( 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 138 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.409 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7354 (mt) REVERT: 2 202 PHE cc_start: 0.5703 (OUTLIER) cc_final: 0.5463 (m-10) REVERT: 3 256 TYR cc_start: 0.7508 (m-80) cc_final: 0.7290 (m-10) REVERT: 3 275 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8204 (t80) REVERT: 3 645 ARG cc_start: 0.5741 (ttt180) cc_final: 0.5502 (ptm160) outliers start: 27 outliers final: 18 residues processed: 126 average time/residue: 0.0892 time to fit residues: 16.9879 Evaluate side-chains 124 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 207 VAL 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 385 VAL 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 485 ILE 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 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 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: 0.8980 chunk 91 optimal weight: 0.6980 chunk 46 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 127 optimal weight: 9.9990 chunk 92 optimal weight: 0.6980 chunk 120 optimal weight: 9.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 168 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 = 0.4301 r_free = 0.4301 target = 0.192634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.176843 restraints weight = 14529.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.172110 restraints weight = 24121.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.170805 restraints weight = 31962.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.170412 restraints weight = 28241.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.169755 restraints weight = 25591.404| |-----------------------------------------------------------------------------| r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11024 Z= 0.217 Angle : 0.619 11.235 15131 Z= 0.316 Chirality : 0.043 0.219 1789 Planarity : 0.004 0.053 1931 Dihedral : 6.087 78.315 2049 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.76 % Allowed : 17.22 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.84 (0.22), residues: 1488 helix: 1.13 (0.20), residues: 679 sheet: -2.42 (0.45), residues: 129 loop : -2.00 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 723 TYR 0.023 0.002 TYR 2 386 PHE 0.021 0.002 PHE 2 250 TRP 0.017 0.001 TRP 2 567 HIS 0.003 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00521 (11007) covalent geometry : angle 0.61919 (15097) SS BOND : bond 0.00246 ( 17) SS BOND : angle 0.63230 ( 34) hydrogen bonds : bond 0.04041 ( 515) hydrogen bonds : angle 4.35165 ( 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 131 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.316 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7507 (mt) REVERT: 2 202 PHE cc_start: 0.5784 (OUTLIER) cc_final: 0.5551 (m-10) REVERT: 3 256 TYR cc_start: 0.7478 (m-80) cc_final: 0.7124 (m-80) REVERT: 3 275 PHE cc_start: 0.8834 (OUTLIER) cc_final: 0.8376 (t80) REVERT: 3 645 ARG cc_start: 0.5763 (ttt180) cc_final: 0.5553 (ptm160) outliers start: 26 outliers final: 18 residues processed: 121 average time/residue: 0.1001 time to fit residues: 17.9287 Evaluate side-chains 121 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 207 VAL Chi-restraints excluded: chain 2 residue 245 MET Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 316 THR 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 485 ILE 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 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 275 PHE Chi-restraints excluded: chain 3 residue 504 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: 0.0870 chunk 120 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 7.9990 chunk 135 optimal weight: 0.7980 chunk 83 optimal weight: 0.0050 chunk 89 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 overall best weight: 0.4372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.196189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.181760 restraints weight = 14487.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.179328 restraints weight = 23716.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.177344 restraints weight = 27390.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.176517 restraints weight = 26460.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.176219 restraints weight = 23097.514| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11024 Z= 0.121 Angle : 0.580 14.267 15131 Z= 0.287 Chirality : 0.041 0.200 1789 Planarity : 0.004 0.052 1931 Dihedral : 5.883 72.954 2049 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.34 % Allowed : 18.28 % 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 aren not related in a simple way. whole: -0.65 (0.22), residues: 1488 helix: 1.32 (0.20), residues: 674 sheet: -2.32 (0.48), residues: 116 loop : -1.93 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 3 723 TYR 0.015 0.001 TYR 2 386 PHE 0.027 0.001 PHE 3 195 TRP 0.015 0.001 TRP 2 567 HIS 0.002 0.000 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00275 (11007) covalent geometry : angle 0.57960 (15097) SS BOND : bond 0.00177 ( 17) SS BOND : angle 0.58858 ( 34) hydrogen bonds : bond 0.03551 ( 515) hydrogen bonds : angle 4.19892 ( 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 133 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7436 (mt) REVERT: 2 202 PHE cc_start: 0.5845 (OUTLIER) cc_final: 0.5587 (m-10) REVERT: 3 256 TYR cc_start: 0.7345 (m-80) cc_final: 0.6970 (m-80) REVERT: 3 275 PHE cc_start: 0.8771 (OUTLIER) cc_final: 0.8394 (t80) REVERT: 3 478 TYR cc_start: 0.5563 (m-10) cc_final: 0.5320 (m-10) outliers start: 22 outliers final: 17 residues processed: 123 average time/residue: 0.0921 time to fit residues: 16.6956 Evaluate side-chains 127 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 245 MET 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 485 ILE 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 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 454 VAL 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: 0.8980 chunk 134 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 139 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 118 optimal weight: 0.0050 chunk 71 optimal weight: 9.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.194362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.179360 restraints weight = 14497.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.176360 restraints weight = 21542.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.174939 restraints weight = 23789.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.174088 restraints weight = 20992.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.173447 restraints weight = 21792.513| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11024 Z= 0.144 Angle : 0.577 13.226 15131 Z= 0.286 Chirality : 0.041 0.262 1789 Planarity : 0.004 0.051 1931 Dihedral : 5.874 71.051 2049 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.44 % Allowed : 18.07 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.22), residues: 1488 helix: 1.36 (0.20), residues: 676 sheet: -2.46 (0.45), residues: 131 loop : -1.90 (0.24), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 467 TYR 0.015 0.002 TYR 2 386 PHE 0.025 0.001 PHE 3 195 TRP 0.012 0.001 TRP 2 567 HIS 0.002 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00340 (11007) covalent geometry : angle 0.57714 (15097) SS BOND : bond 0.00180 ( 17) SS BOND : angle 0.55579 ( 34) hydrogen bonds : bond 0.03550 ( 515) hydrogen bonds : angle 4.16327 ( 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 137 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7461 (mt) REVERT: 2 202 PHE cc_start: 0.5820 (OUTLIER) cc_final: 0.5535 (m-10) REVERT: 2 388 MET cc_start: 0.7944 (tpp) cc_final: 0.7382 (tpt) REVERT: 3 256 TYR cc_start: 0.7399 (m-80) cc_final: 0.6993 (m-80) REVERT: 3 275 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8464 (t80) REVERT: 3 478 TYR cc_start: 0.5554 (m-10) cc_final: 0.5309 (m-10) outliers start: 23 outliers final: 19 residues processed: 126 average time/residue: 0.0871 time to fit residues: 17.0355 Evaluate side-chains 131 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 245 MET 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 485 ILE 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 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 276 MET Chi-restraints excluded: chain 3 residue 435 LEU Chi-restraints excluded: chain 3 residue 454 VAL Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 639 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: 7.9990 chunk 40 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 132 optimal weight: 0.7980 chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 107 optimal weight: 0.0050 chunk 8 optimal weight: 0.9980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.194889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.179510 restraints weight = 14475.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.176851 restraints weight = 24167.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.175390 restraints weight = 24616.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.174612 restraints weight = 23807.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.174012 restraints weight = 19991.572| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11024 Z= 0.134 Angle : 0.581 14.084 15131 Z= 0.289 Chirality : 0.041 0.263 1789 Planarity : 0.004 0.051 1931 Dihedral : 5.817 67.396 2049 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 2.44 % Allowed : 18.60 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.22), residues: 1488 helix: 1.38 (0.20), residues: 681 sheet: -2.33 (0.47), residues: 125 loop : -1.89 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 467 TYR 0.016 0.001 TYR 2 386 PHE 0.037 0.001 PHE 3 195 TRP 0.011 0.001 TRP 2 567 HIS 0.002 0.001 HIS 2 390 Details of bonding type rmsd covalent geometry : bond 0.00313 (11007) covalent geometry : angle 0.58080 (15097) SS BOND : bond 0.00159 ( 17) SS BOND : angle 0.49012 ( 34) hydrogen bonds : bond 0.03453 ( 515) hydrogen bonds : angle 4.12990 ( 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 133 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7395 (mt) REVERT: 2 388 MET cc_start: 0.7962 (tpp) cc_final: 0.7364 (tpt) REVERT: 3 256 TYR cc_start: 0.7388 (m-80) cc_final: 0.7060 (m-80) REVERT: 3 275 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8472 (t80) REVERT: 3 407 MET cc_start: 0.6871 (ttp) cc_final: 0.6664 (ttp) REVERT: 3 478 TYR cc_start: 0.5689 (m-10) cc_final: 0.5412 (m-10) outliers start: 23 outliers final: 17 residues processed: 122 average time/residue: 0.0900 time to fit residues: 16.6167 Evaluate side-chains 123 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 485 ILE 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 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 454 VAL Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 639 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: 1.9990 chunk 121 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 140 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 97 HIS 3 357 GLN 3 467 ASN ** 3 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.191244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.175741 restraints weight = 14538.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.172420 restraints weight = 24289.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.172147 restraints weight = 26778.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.171662 restraints weight = 24208.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.171079 restraints weight = 20185.263| |-----------------------------------------------------------------------------| r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6777 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11024 Z= 0.241 Angle : 0.652 13.791 15131 Z= 0.330 Chirality : 0.044 0.266 1789 Planarity : 0.004 0.051 1931 Dihedral : 6.060 69.338 2049 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.13 % Allowed : 19.45 % 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 aren not related in a simple way. whole: -0.73 (0.22), residues: 1488 helix: 1.24 (0.20), residues: 687 sheet: -2.46 (0.45), residues: 127 loop : -1.98 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 2 467 TYR 0.024 0.002 TYR 3 256 PHE 0.035 0.002 PHE 3 195 TRP 0.009 0.001 TRP 2 567 HIS 0.004 0.001 HIS 3 498 Details of bonding type rmsd covalent geometry : bond 0.00579 (11007) covalent geometry : angle 0.65231 (15097) SS BOND : bond 0.00251 ( 17) SS BOND : angle 0.64437 ( 34) hydrogen bonds : bond 0.03900 ( 515) hydrogen bonds : angle 4.30314 ( 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 125 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7533 (mt) REVERT: 3 256 TYR cc_start: 0.7611 (m-80) cc_final: 0.7239 (m-80) REVERT: 3 275 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8433 (t80) REVERT: 3 478 TYR cc_start: 0.5712 (m-10) cc_final: 0.5488 (m-10) outliers start: 20 outliers final: 13 residues processed: 118 average time/residue: 0.0922 time to fit residues: 16.4148 Evaluate side-chains 119 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.401 ------------------------------------------------------------------------------- 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 485 ILE Chi-restraints excluded: chain 2 residue 495 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 639 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 98 optimal weight: 0.9990 chunk 125 optimal weight: 0.0670 chunk 16 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 0.0770 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 0.2980 chunk 0 optimal weight: 5.9990 overall best weight: 0.2276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 97 HIS ** 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 = 0.4338 r_free = 0.4338 target = 0.196532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.183827 restraints weight = 14804.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.180623 restraints weight = 24327.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.179325 restraints weight = 21229.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.177382 restraints weight = 23012.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.176626 restraints weight = 22688.698| |-----------------------------------------------------------------------------| r_work (final): 0.4127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11024 Z= 0.114 Angle : 0.587 14.742 15131 Z= 0.292 Chirality : 0.041 0.270 1789 Planarity : 0.004 0.051 1931 Dihedral : 5.816 63.026 2049 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.38 % Favored : 93.55 % Rotamer: Outliers : 1.91 % Allowed : 19.98 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.22), residues: 1488 helix: 1.45 (0.20), residues: 677 sheet: -2.27 (0.48), residues: 115 loop : -1.89 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 2 467 TYR 0.016 0.001 TYR 2 386 PHE 0.035 0.001 PHE 3 195 TRP 0.013 0.001 TRP 3 499 HIS 0.011 0.001 HIS 2 592 Details of bonding type rmsd covalent geometry : bond 0.00250 (11007) covalent geometry : angle 0.58727 (15097) SS BOND : bond 0.00160 ( 17) SS BOND : angle 0.49752 ( 34) hydrogen bonds : bond 0.03383 ( 515) hydrogen bonds : angle 4.13777 ( 1482) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1632.28 seconds wall clock time: 28 minutes 57.80 seconds (1737.80 seconds total)