Starting phenix.real_space_refine on Sat Nov 16 11:09:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd1_36172/11_2024/8jd1_36172.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd1_36172/11_2024/8jd1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd1_36172/11_2024/8jd1_36172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd1_36172/11_2024/8jd1_36172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd1_36172/11_2024/8jd1_36172.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd1_36172/11_2024/8jd1_36172.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 12, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 14, 'GLU:plan': 14, 'ARG:plan': 24} 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: {'GLN:plan1': 5, 'HIS:plan': 2, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 11, 'GLU:plan': 9, 'ARG:plan': 11} 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: 7.42, per 1000 atoms: 0.69 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: 2.79 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.32 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: 3.42 Time building geometry restraints manager: 3.26 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: 2.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.900 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.840 ------------------------------------------------------------------------------- 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 11007 Z= 0.142 Angle : 0.495 5.794 15097 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 : 6.47 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (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 TRP 0.014 0.001 TRP 3 529 HIS 0.001 0.000 HIS 3 485 PHE 0.017 0.001 PHE 2 190 TYR 0.009 0.001 TYR 3 539 ARG 0.002 0.000 ARG 2 360 *********************** 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 : 1.178 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.2016 time to fit residues: 46.0902 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 : 1.201 ------------------------------------------------------------------------------- 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 126 optimal weight: 8.9990 chunk 113 optimal weight: 0.0970 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 60 optimal weight: 40.0000 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- 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** 3 197 GLN 3 232 GLN 3 386 GLN 3 402 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.096 11007 Z= 0.449 Angle : 0.680 9.698 15097 Z= 0.359 Chirality : 0.045 0.241 1789 Planarity : 0.005 0.044 1931 Dihedral : 6.379 86.198 2052 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.91 % Allowed : 9.35 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.22), residues: 1488 helix: 0.87 (0.20), residues: 659 sheet: -2.62 (0.42), residues: 144 loop : -2.00 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP 2 697 HIS 0.005 0.001 HIS 3 498 PHE 0.019 0.002 PHE 2 181 TYR 0.024 0.002 TYR 3 222 ARG 0.005 0.001 ARG 2 156 *********************** 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 144 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: 3 275 PHE cc_start: 0.8632 (OUTLIER) cc_final: 0.8358 (t80) REVERT: 3 644 ARG cc_start: 0.8386 (mtt180) cc_final: 0.8172 (mtt90) REVERT: 3 645 ARG cc_start: 0.6711 (ttt180) cc_final: 0.5981 (ptm160) outliers start: 18 outliers final: 14 residues processed: 138 average time/residue: 0.2249 time to fit residues: 45.1480 Evaluate side-chains 115 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 78 LEU Chi-restraints excluded: chain 2 residue 207 VAL Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 304 VAL Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 428 PHE 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.5980 chunk 42 optimal weight: 0.6980 chunk 113 optimal weight: 0.0000 chunk 92 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 0.0980 chunk 147 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 135 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 87 HIS 2 97 HIS 2 414 ASN ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11007 Z= 0.187 Angle : 0.562 10.310 15097 Z= 0.287 Chirality : 0.041 0.152 1789 Planarity : 0.004 0.049 1931 Dihedral : 6.081 86.437 2049 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.44 % Allowed : 12.43 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.22), residues: 1488 helix: 1.03 (0.20), residues: 656 sheet: -2.43 (0.43), residues: 144 loop : -1.99 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP 2 567 HIS 0.002 0.001 HIS 3 485 PHE 0.018 0.001 PHE 2 250 TYR 0.014 0.001 TYR 3 256 ARG 0.005 0.000 ARG 2 57 *********************** 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 142 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.198 Fit side-chains REVERT: 3 239 ILE cc_start: 0.7342 (pt) cc_final: 0.7077 (pt) REVERT: 3 256 TYR cc_start: 0.7246 (m-10) cc_final: 0.6724 (m-10) REVERT: 3 275 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.8022 (t80) REVERT: 3 422 MET cc_start: 0.7380 (mmm) cc_final: 0.7142 (mmm) REVERT: 3 645 ARG cc_start: 0.6607 (ttt180) cc_final: 0.6056 (ptm160) outliers start: 23 outliers final: 11 residues processed: 133 average time/residue: 0.2215 time to fit residues: 42.8017 Evaluate side-chains 117 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 105 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 201 PHE Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 446 PHE Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 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 544 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 129 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 87 HIS ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 168 GLN 3 357 GLN 3 467 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.115 11007 Z= 0.674 Angle : 0.813 14.549 15097 Z= 0.423 Chirality : 0.050 0.345 1789 Planarity : 0.006 0.053 1931 Dihedral : 6.637 82.393 2049 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer: Outliers : 3.72 % Allowed : 15.09 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.22), residues: 1488 helix: 0.69 (0.20), residues: 663 sheet: -2.80 (0.42), residues: 137 loop : -2.12 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 2 563 HIS 0.007 0.002 HIS 3 498 PHE 0.019 0.003 PHE 2 428 TYR 0.033 0.003 TYR 3 256 ARG 0.006 0.001 ARG 3 723 *********************** 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 143 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 108 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8004 (mm) REVERT: 3 275 PHE cc_start: 0.8992 (OUTLIER) cc_final: 0.8433 (t80) REVERT: 3 423 LYS cc_start: 0.8575 (mmmt) cc_final: 0.8226 (mptt) outliers start: 35 outliers final: 24 residues processed: 132 average time/residue: 0.2152 time to fit residues: 42.0144 Evaluate side-chains 127 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 207 VAL Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 385 VAL Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 450 ILE 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 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 247 VAL Chi-restraints excluded: chain 3 residue 271 VAL Chi-restraints excluded: chain 3 residue 272 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 544 PHE Chi-restraints excluded: chain 3 residue 596 THR Chi-restraints excluded: chain 3 residue 643 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 120 optimal weight: 10.0000 chunk 82 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 168 GLN 3 197 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11007 Z= 0.263 Angle : 0.603 10.696 15097 Z= 0.306 Chirality : 0.042 0.167 1789 Planarity : 0.004 0.054 1931 Dihedral : 6.276 77.352 2049 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.44 % Allowed : 18.92 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1488 helix: 0.90 (0.20), residues: 672 sheet: -2.48 (0.47), residues: 116 loop : -2.09 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 2 563 HIS 0.004 0.001 HIS 2 390 PHE 0.011 0.001 PHE 2 269 TYR 0.019 0.002 TYR 2 386 ARG 0.004 0.000 ARG 3 723 *********************** 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 132 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 1.224 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7555 (mt) REVERT: 2 388 MET cc_start: 0.7857 (tpp) cc_final: 0.7200 (tpt) REVERT: 3 256 TYR cc_start: 0.7896 (m-80) cc_final: 0.7632 (m-80) REVERT: 3 275 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8435 (t80) REVERT: 3 645 ARG cc_start: 0.6614 (ttt180) cc_final: 0.6197 (ptm160) outliers start: 23 outliers final: 14 residues processed: 122 average time/residue: 0.2262 time to fit residues: 41.8109 Evaluate side-chains 122 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 592 HIS Chi-restraints excluded: chain 2 residue 639 LEU 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 289 SER Chi-restraints excluded: chain 3 residue 435 LEU Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 646 LEU 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 48 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 28 optimal weight: 0.1980 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 145 optimal weight: 9.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 0.5980 chunk 139 optimal weight: 20.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11007 Z= 0.240 Angle : 0.588 11.657 15097 Z= 0.297 Chirality : 0.042 0.187 1789 Planarity : 0.004 0.054 1931 Dihedral : 6.128 72.878 2049 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.87 % Allowed : 19.45 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1488 helix: 1.10 (0.20), residues: 667 sheet: -2.61 (0.46), residues: 120 loop : -2.00 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 2 563 HIS 0.003 0.001 HIS 2 390 PHE 0.012 0.001 PHE 2 269 TYR 0.018 0.002 TYR 2 386 ARG 0.004 0.000 ARG 3 723 *********************** 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 137 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 110 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7523 (mt) REVERT: 2 388 MET cc_start: 0.7698 (tpp) cc_final: 0.7465 (tpt) REVERT: 3 34 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8146 (mmmt) REVERT: 3 256 TYR cc_start: 0.7929 (m-80) cc_final: 0.7653 (m-80) REVERT: 3 275 PHE cc_start: 0.8907 (OUTLIER) cc_final: 0.8426 (t80) REVERT: 3 423 LYS cc_start: 0.8480 (mmmt) cc_final: 0.8222 (mptt) REVERT: 3 645 ARG cc_start: 0.6656 (ttt180) cc_final: 0.6326 (ptm160) outliers start: 27 outliers final: 19 residues processed: 130 average time/residue: 0.2240 time to fit residues: 43.9056 Evaluate side-chains 129 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 385 VAL Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 592 HIS Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 34 LYS 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 247 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 310 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 144 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 66 optimal weight: 20.0000 chunk 89 optimal weight: 0.4980 chunk 57 optimal weight: 7.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11007 Z= 0.348 Angle : 0.638 14.070 15097 Z= 0.321 Chirality : 0.043 0.222 1789 Planarity : 0.004 0.053 1931 Dihedral : 6.209 71.629 2049 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 3.08 % Allowed : 19.66 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1488 helix: 1.05 (0.20), residues: 678 sheet: -2.77 (0.42), residues: 134 loop : -2.03 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 697 HIS 0.004 0.001 HIS 2 390 PHE 0.013 0.001 PHE 2 269 TYR 0.020 0.002 TYR 2 386 ARG 0.004 0.000 ARG 3 723 *********************** 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 136 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7632 (mt) REVERT: 2 245 MET cc_start: 0.6293 (pmm) cc_final: 0.5983 (pmm) REVERT: 3 34 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8197 (mmmt) REVERT: 3 256 TYR cc_start: 0.7939 (m-80) cc_final: 0.7595 (m-80) REVERT: 3 275 PHE cc_start: 0.8943 (OUTLIER) cc_final: 0.8459 (t80) REVERT: 3 645 ARG cc_start: 0.6680 (ttt180) cc_final: 0.6337 (ptm160) outliers start: 29 outliers final: 21 residues processed: 128 average time/residue: 0.2104 time to fit residues: 40.1816 Evaluate side-chains 129 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 105 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 385 VAL Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 484 LEU Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 34 LYS 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 247 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 289 SER Chi-restraints excluded: chain 3 residue 310 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 0.3980 chunk 71 optimal weight: 4.9990 chunk 13 optimal weight: 0.0370 chunk 113 optimal weight: 0.0770 chunk 131 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 126 optimal weight: 8.9990 overall best weight: 0.2816 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11007 Z= 0.175 Angle : 0.589 12.922 15097 Z= 0.292 Chirality : 0.041 0.225 1789 Planarity : 0.004 0.053 1931 Dihedral : 5.965 65.081 2049 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.55 % Allowed : 20.30 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.22), residues: 1488 helix: 1.23 (0.20), residues: 667 sheet: -2.58 (0.44), residues: 126 loop : -1.90 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 563 HIS 0.004 0.001 HIS 2 592 PHE 0.013 0.001 PHE 2 269 TYR 0.014 0.001 TYR 3 743 ARG 0.004 0.000 ARG 3 723 *********************** 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 142 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.237 Fit side-chains revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7539 (mt) REVERT: 2 388 MET cc_start: 0.7684 (tpp) cc_final: 0.7387 (tpt) REVERT: 3 31 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.6444 (ptm160) REVERT: 3 256 TYR cc_start: 0.7777 (m-80) cc_final: 0.7486 (m-80) REVERT: 3 275 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.8440 (t80) REVERT: 3 614 LEU cc_start: 0.7346 (OUTLIER) cc_final: 0.6991 (pp) REVERT: 3 645 ARG cc_start: 0.6751 (ttt180) cc_final: 0.6472 (ptm160) outliers start: 24 outliers final: 14 residues processed: 135 average time/residue: 0.2200 time to fit residues: 43.8565 Evaluate side-chains 128 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 31 ARG Chi-restraints excluded: chain 3 residue 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 247 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 614 LEU Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 798 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 9.9990 chunk 138 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 0.0970 chunk 41 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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** ** 2 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11007 Z= 0.235 Angle : 0.599 14.119 15097 Z= 0.297 Chirality : 0.042 0.266 1789 Planarity : 0.004 0.052 1931 Dihedral : 5.954 63.732 2049 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.74 % Rotamer: Outliers : 2.55 % Allowed : 20.72 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1488 helix: 1.31 (0.20), residues: 665 sheet: -2.49 (0.44), residues: 134 loop : -1.92 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 697 HIS 0.007 0.001 HIS 2 592 PHE 0.013 0.001 PHE 2 269 TYR 0.013 0.001 TYR 3 743 ARG 0.004 0.000 ARG 3 723 *********************** 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 136 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 112 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7493 (mt) REVERT: 2 388 MET cc_start: 0.7774 (tpp) cc_final: 0.7466 (tpt) REVERT: 3 31 ARG cc_start: 0.6667 (OUTLIER) cc_final: 0.6431 (ptm160) REVERT: 3 256 TYR cc_start: 0.7848 (m-80) cc_final: 0.7576 (m-80) REVERT: 3 275 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8494 (t80) REVERT: 3 614 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6993 (pp) REVERT: 3 645 ARG cc_start: 0.6775 (ttt180) cc_final: 0.6472 (ptm160) outliers start: 24 outliers final: 15 residues processed: 128 average time/residue: 0.2126 time to fit residues: 40.7930 Evaluate side-chains 131 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 31 ARG Chi-restraints excluded: chain 3 residue 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 247 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 614 LEU 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 67 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 0.6980 chunk 137 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- 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** ** 2 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11007 Z= 0.249 Angle : 0.618 15.652 15097 Z= 0.303 Chirality : 0.043 0.264 1789 Planarity : 0.004 0.053 1931 Dihedral : 5.929 61.917 2049 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.74 % Rotamer: Outliers : 2.13 % Allowed : 21.15 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.22), residues: 1488 helix: 1.28 (0.20), residues: 672 sheet: -2.54 (0.43), residues: 134 loop : -1.89 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 697 HIS 0.003 0.001 HIS 2 390 PHE 0.013 0.001 PHE 2 269 TYR 0.014 0.002 TYR 2 386 ARG 0.004 0.000 ARG 3 723 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2976 Ramachandran restraints generated. 1488 Oldfield, 0 Emsley, 1488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7518 (mt) REVERT: 2 388 MET cc_start: 0.7798 (tpp) cc_final: 0.7490 (tpt) REVERT: 3 31 ARG cc_start: 0.6683 (OUTLIER) cc_final: 0.6469 (ptm160) REVERT: 3 256 TYR cc_start: 0.7864 (m-80) cc_final: 0.7606 (m-80) REVERT: 3 275 PHE cc_start: 0.8892 (OUTLIER) cc_final: 0.8493 (t80) REVERT: 3 614 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6909 (pp) REVERT: 3 645 ARG cc_start: 0.6796 (ttt180) cc_final: 0.6500 (ptm160) outliers start: 20 outliers final: 15 residues processed: 123 average time/residue: 0.2136 time to fit residues: 39.1436 Evaluate side-chains 128 residues out of total 1285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 89 LEU Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 294 SER Chi-restraints excluded: chain 2 residue 316 THR Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 441 VAL Chi-restraints excluded: chain 2 residue 495 LEU Chi-restraints excluded: chain 2 residue 639 LEU Chi-restraints excluded: chain 3 residue 31 ARG Chi-restraints excluded: chain 3 residue 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 247 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 276 MET Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 614 LEU 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 109 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 122 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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** ** 2 592 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.193977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.178612 restraints weight = 14709.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.176179 restraints weight = 24695.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.175444 restraints weight = 20668.184| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6704 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11007 Z= 0.250 Angle : 0.613 14.344 15097 Z= 0.301 Chirality : 0.042 0.271 1789 Planarity : 0.004 0.053 1931 Dihedral : 5.898 59.773 2049 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.19 % Favored : 92.74 % Rotamer: Outliers : 2.34 % Allowed : 20.83 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.22), residues: 1488 helix: 1.29 (0.20), residues: 674 sheet: -2.43 (0.44), residues: 128 loop : -1.91 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 697 HIS 0.002 0.001 HIS 2 390 PHE 0.016 0.001 PHE 2 422 TYR 0.014 0.002 TYR 2 386 ARG 0.004 0.000 ARG 3 723 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2092.89 seconds wall clock time: 45 minutes 47.86 seconds (2747.86 seconds total)