Starting phenix.real_space_refine on Fri Mar 15 05:59:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd1_36172/03_2024/8jd1_36172_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd1_36172/03_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_36172/03_2024/8jd1_36172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd1_36172/03_2024/8jd1_36172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd1_36172/03_2024/8jd1_36172_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd1_36172/03_2024/8jd1_36172_updated.pdb" } 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 Residue "3 ASP 433": "OD1" <-> "OD2" Residue "3 TYR 478": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 632": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 1101": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10766 Number of models: 1 Model: "" Number of chains: 4 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: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 206 Unusual residues: {'CLR': 7} Classifications: {'peptide': 1, 'undetermined': 7} Modifications used: {'COO': 1} Link IDs: {None: 7} Time building chain proxies: 6.53, per 1000 atoms: 0.61 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 - 3.50 Amino acid : False - 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: 4.33 Conformation dependent library (CDL) restraints added in 2.3 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... running ksdssp... Secondary structure from input PDB file: 47 helices and 10 sheets defined 44.8% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain '2' and resid 59 through 74 removed outlier: 3.615A pdb=" N ARG 2 74 " --> pdb=" O ASP 2 70 " (cutoff:3.500A) Processing helix chain '2' and resid 95 through 107 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) Processing helix chain '2' and resid 145 through 155 Processing helix chain '2' and resid 170 through 172 No H-bonds generated for 'chain '2' and resid 170 through 172' Processing helix chain '2' and resid 190 through 201 removed outlier: 3.559A pdb=" N PHE 2 201 " --> pdb=" O ILE 2 198 " (cutoff:3.500A) Processing helix chain '2' and resid 215 through 228 Processing helix chain '2' and resid 247 through 257 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 272 through 285 Processing helix chain '2' and resid 295 through 297 No H-bonds generated for 'chain '2' and resid 295 through 297' Processing helix chain '2' and resid 301 through 304 No H-bonds generated for 'chain '2' and resid 301 through 304' Processing helix chain '2' and resid 326 through 333 removed outlier: 3.558A pdb=" N SER 2 333 " --> pdb=" O SER 2 329 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 353 Processing helix chain '2' and resid 357 through 359 No H-bonds generated for 'chain '2' and resid 357 through 359' Processing helix chain '2' and resid 378 through 399 Processing helix chain '2' and resid 408 through 410 No H-bonds generated for 'chain '2' and resid 408 through 410' Processing helix chain '2' and resid 415 through 422 removed outlier: 3.596A pdb=" N LYS 2 420 " --> pdb=" O ARG 2 416 " (cutoff:3.500A) Processing helix chain '2' and resid 482 through 484 No H-bonds generated for 'chain '2' and resid 482 through 484' Processing helix chain '2' and resid 569 through 592 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 597 through 599 No H-bonds generated for 'chain '2' and resid 597 through 599' Processing helix chain '2' and resid 603 through 623 removed outlier: 3.826A pdb=" N PHE 2 621 " --> pdb=" O TYR 2 617 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE 2 623 " --> pdb=" O MET 2 619 " (cutoff:3.500A) Processing helix chain '2' and resid 629 through 659 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 676 through 701 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 722 through 749 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) Processing helix chain '2' and resid 757 through 781 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 789 through 809 removed outlier: 3.603A pdb=" N CYS 2 795 " --> pdb=" O THR 2 791 " (cutoff:3.500A) Processing helix chain '2' and resid 811 through 816 Processing helix chain '3' and resid 66 through 80 Processing helix chain '3' and resid 102 through 114 removed outlier: 3.594A pdb=" N GLU 3 107 " --> pdb=" O THR 3 103 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N PHE 3 112 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG 3 114 " --> pdb=" O LEU 3 110 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 164 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 196 through 207 Processing helix chain '3' and resid 221 through 236 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 256 through 264 Processing helix chain '3' and resid 278 through 291 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 331 through 338 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 349 through 358 removed outlier: 3.940A pdb=" N ARG 3 352 " --> pdb=" O PRO 3 349 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP 3 355 " --> pdb=" O ARG 3 352 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS 3 358 " --> pdb=" O TRP 3 355 " (cutoff:3.500A) Processing helix chain '3' and resid 381 through 383 No H-bonds generated for 'chain '3' and resid 381 through 383' Processing helix chain '3' and resid 388 through 411 removed outlier: 4.281A pdb=" N MET 3 391 " --> pdb=" O SER 3 388 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N PHE 3 392 " --> pdb=" O LYS 3 389 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET 3 400 " --> pdb=" O VAL 3 397 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU 3 404 " --> pdb=" O ALA 3 401 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN 3 408 " --> pdb=" O HIS 3 405 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ARG 3 409 " --> pdb=" O LYS 3 406 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR 3 410 " --> pdb=" O MET 3 407 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU 3 411 " --> pdb=" O GLN 3 408 " (cutoff:3.500A) Processing helix chain '3' and resid 420 through 422 No H-bonds generated for 'chain '3' and resid 420 through 422' Processing helix chain '3' and resid 428 through 437 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) removed outlier: 4.238A pdb=" N LEU 3 436 " --> pdb=" O LYS 3 432 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS 3 437 " --> pdb=" O ASP 3 433 " (cutoff:3.500A) Processing helix chain '3' and resid 576 through 601 Proline residue: 3 580 - end of helix Processing helix chain '3' and resid 614 through 632 removed outlier: 3.602A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) Processing helix chain '3' and resid 638 through 663 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 704 removed outlier: 3.809A pdb=" N SER 3 686 " --> pdb=" O PHE 3 682 " (cutoff:3.500A) Processing helix chain '3' and resid 708 through 710 No H-bonds generated for 'chain '3' and resid 708 through 710' Processing helix chain '3' and resid 734 through 758 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) removed outlier: 3.541A pdb=" N ALA 3 755 " --> pdb=" O CYS 3 751 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE 3 756 " --> pdb=" O THR 3 752 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N LYS 3 757 " --> pdb=" O VAL 3 753 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR 3 758 " --> pdb=" O TYR 3 754 " (cutoff:3.500A) Processing helix chain '3' and resid 762 through 791 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 800 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= A, 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) Processing sheet with id= B, first strand: chain '2' and resid 35 through 37 Processing sheet with id= C, first strand: chain '2' and resid 162 through 164 Processing sheet with id= D, first strand: chain '2' and resid 265 through 268 removed outlier: 6.867A pdb=" N THR 2 290 " --> pdb=" O ALA 2 266 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU 2 268 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL 2 292 " --> pdb=" O LEU 2 268 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain '2' and resid 317 through 319 removed outlier: 3.513A pdb=" N TYR 2 453 " --> pdb=" O TRP 2 474 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEU 2 459 " --> pdb=" O TYR 2 468 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR 2 468 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '2' and resid 206 through 210 removed outlier: 7.122A pdb=" N CYS 2 234 " --> pdb=" O VAL 2 207 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N THR 2 209 " --> pdb=" O CYS 2 234 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ALA 2 236 " --> pdb=" O THR 2 209 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain '3' and resid 91 through 97 removed outlier: 6.473A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N GLY 3 42 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N VAL 3 145 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU 3 44 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 214 through 217 removed outlier: 3.855A pdb=" N SER 3 214 " --> pdb=" O VAL 3 271 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL 3 216 " --> pdb=" O VAL 3 273 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE 3 275 " --> pdb=" O VAL 3 216 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N THR 3 296 " --> pdb=" O VAL 3 272 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU 3 274 " --> pdb=" O THR 3 296 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL 3 298 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 321 through 325 removed outlier: 4.261A pdb=" N TYR 3 466 " --> pdb=" O TRP 3 486 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL 3 468 " --> pdb=" O GLY 3 484 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY 3 484 " --> pdb=" O VAL 3 468 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain '3' and resid 716 through 718 430 hydrogen bonds defined for protein. 1146 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: 3.17 Time building geometry restraints manager: 4.68 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: 99.58 - 106.47: 337 106.47 - 113.37: 6085 113.37 - 120.26: 3654 120.26 - 127.16: 4902 127.16 - 134.05: 119 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: 1862 2.76 - 3.30: 10931 3.30 - 3.83: 17247 3.83 - 4.37: 19348 4.37 - 4.90: 33068 Nonbonded interactions: 82456 Sorted by model distance: nonbonded pdb=" O TYR 3 626 " pdb=" OG1 THR 3 629 " model vdw 2.228 2.440 nonbonded pdb=" OH TYR 3 384 " pdb=" OE1 GLN 3 386 " model vdw 2.233 2.440 nonbonded pdb=" OG1 THR 3 792 " pdb=" O GLN 3 799 " model vdw 2.249 2.440 nonbonded pdb=" OG SER 3 327 " pdb=" O SER 3 388 " model vdw 2.254 2.440 nonbonded pdb=" OG SER 3 218 " pdb=" OD2 ASP 3 280 " model vdw 2.285 2.440 ... (remaining 82451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 5.470 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: 10.700 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 32.290 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.100 ------------------------------------------------------------------------------- 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= 0.138 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 fitting. 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: 0.1978 time to fit residues: 44.9554 Evaluate side-chains 115 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 114 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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: 2.9990 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 20.0000 chunk 117 optimal weight: 2.9990 chunk 45 optimal weight: 30.0000 chunk 71 optimal weight: 8.9990 chunk 87 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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** 3 168 GLN 3 402 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 11007 Z= 0.450 Angle : 0.674 10.059 15097 Z= 0.355 Chirality : 0.045 0.252 1789 Planarity : 0.005 0.047 1931 Dihedral : 6.509 86.904 2052 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 2.34 % Allowed : 9.78 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.20), residues: 643 sheet: -2.73 (0.42), residues: 146 loop : -2.03 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP 2 697 HIS 0.006 0.001 HIS 3 498 PHE 0.018 0.002 PHE 2 181 TYR 0.025 0.003 TYR 3 222 ARG 0.009 0.001 ARG 2 636 *********************** 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 146 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 275 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8299 (t80) REVERT: 3 645 ARG cc_start: 0.6698 (ttt180) cc_final: 0.5988 (ptm160) outliers start: 22 outliers final: 16 residues processed: 139 average time/residue: 0.2282 time to fit residues: 45.8588 Evaluate side-chains 115 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 78 LEU Chi-restraints excluded: chain 2 residue 167 SER 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 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 247 VAL Chi-restraints excluded: chain 3 residue 275 PHE Chi-restraints excluded: chain 3 residue 544 PHE Chi-restraints excluded: chain 3 residue 738 LEU Chi-restraints excluded: chain 2 residue 1101 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 chunk 109 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** 2 414 ASN 3 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11007 Z= 0.247 Angle : 0.561 9.906 15097 Z= 0.287 Chirality : 0.041 0.148 1789 Planarity : 0.004 0.051 1931 Dihedral : 6.350 87.896 2052 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 2.76 % Allowed : 13.60 % Favored : 83.63 % 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: -1.23 (0.22), residues: 1488 helix: 0.81 (0.21), residues: 635 sheet: -2.71 (0.43), residues: 138 loop : -1.98 (0.22), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 3 529 HIS 0.003 0.001 HIS 2 390 PHE 0.020 0.002 PHE 2 250 TYR 0.019 0.002 TYR 2 386 ARG 0.004 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 133 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 107 time to evaluate : 0.933 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7793 (mm) REVERT: 3 256 TYR cc_start: 0.7430 (m-80) cc_final: 0.6848 (m-10) REVERT: 3 275 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.8059 (t80) REVERT: 3 645 ARG cc_start: 0.6665 (ttt180) cc_final: 0.6175 (ptm160) outliers start: 26 outliers final: 16 residues processed: 123 average time/residue: 0.2099 time to fit residues: 38.6426 Evaluate side-chains 117 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 167 SER Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 304 VAL 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 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 Chi-restraints excluded: chain 3 residue 603 ASN Chi-restraints excluded: chain 3 residue 738 LEU Chi-restraints excluded: chain 3 residue 802 THR Chi-restraints excluded: chain 2 residue 1101 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 91 optimal weight: 0.5980 chunk 136 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 129 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 11007 Z= 0.387 Angle : 0.623 9.206 15097 Z= 0.322 Chirality : 0.043 0.236 1789 Planarity : 0.004 0.051 1931 Dihedral : 6.500 89.678 2052 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 3.93 % Allowed : 14.77 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.22), residues: 1488 helix: 0.72 (0.21), residues: 646 sheet: -2.55 (0.43), residues: 133 loop : -2.09 (0.22), residues: 709 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 0.014 0.002 PHE 2 250 TYR 0.021 0.002 TYR 2 386 ARG 0.004 0.000 ARG 2 57 *********************** 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 142 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 105 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7927 (mm) REVERT: 2 245 MET cc_start: 0.6636 (pmm) cc_final: 0.6150 (pmm) REVERT: 2 438 HIS cc_start: 0.2136 (OUTLIER) cc_final: 0.0875 (t-170) REVERT: 3 256 TYR cc_start: 0.7816 (m-80) cc_final: 0.7418 (m-80) REVERT: 3 275 PHE cc_start: 0.8802 (OUTLIER) cc_final: 0.8365 (t80) REVERT: 3 423 LYS cc_start: 0.8635 (mmmt) cc_final: 0.8156 (mptt) REVERT: 3 645 ARG cc_start: 0.6781 (ttt180) cc_final: 0.6129 (ptm160) outliers start: 37 outliers final: 22 residues processed: 133 average time/residue: 0.1845 time to fit residues: 36.8132 Evaluate side-chains 128 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 167 SER 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 316 THR Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 385 VAL Chi-restraints excluded: chain 2 residue 438 HIS 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 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 243 THR 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 504 VAL Chi-restraints excluded: chain 3 residue 603 ASN Chi-restraints excluded: chain 3 residue 738 LEU Chi-restraints excluded: chain 3 residue 802 THR Chi-restraints excluded: chain 2 residue 1101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 2 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 100 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 74 optimal weight: 0.0030 chunk 130 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.0592 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11007 Z= 0.294 Angle : 0.583 9.656 15097 Z= 0.298 Chirality : 0.042 0.178 1789 Planarity : 0.004 0.051 1931 Dihedral : 6.417 88.601 2052 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 3.40 % Allowed : 17.22 % 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 (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: -1.22 (0.22), residues: 1488 helix: 0.80 (0.21), residues: 645 sheet: -2.62 (0.45), residues: 128 loop : -2.04 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP 2 567 HIS 0.003 0.001 HIS 2 390 PHE 0.033 0.002 PHE 3 195 TYR 0.020 0.002 TYR 2 386 ARG 0.003 0.000 ARG 2 57 *********************** 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 142 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 1.228 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8240 (OUTLIER) cc_final: 0.7941 (mm) REVERT: 2 438 HIS cc_start: 0.2269 (OUTLIER) cc_final: 0.0823 (t-170) REVERT: 3 256 TYR cc_start: 0.7918 (m-80) cc_final: 0.7572 (m-80) REVERT: 3 275 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.8365 (t80) REVERT: 3 632 PHE cc_start: 0.8236 (m-80) cc_final: 0.8014 (m-80) REVERT: 3 645 ARG cc_start: 0.6856 (ttt180) cc_final: 0.6481 (ptm160) outliers start: 32 outliers final: 22 residues processed: 137 average time/residue: 0.1948 time to fit residues: 40.3643 Evaluate side-chains 131 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 167 SER 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 316 THR Chi-restraints excluded: chain 2 residue 326 ASP Chi-restraints excluded: chain 2 residue 385 VAL Chi-restraints excluded: chain 2 residue 438 HIS 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 190 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 243 THR 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 504 VAL Chi-restraints excluded: chain 3 residue 738 LEU Chi-restraints excluded: chain 3 residue 802 THR Chi-restraints excluded: chain 2 residue 1101 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 145 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 139 optimal weight: 20.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.3278 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= 0.275 Angle : 0.583 11.246 15097 Z= 0.296 Chirality : 0.042 0.227 1789 Planarity : 0.004 0.050 1931 Dihedral : 6.367 88.204 2052 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 3.29 % Allowed : 19.02 % 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: -1.15 (0.22), residues: 1488 helix: 0.85 (0.21), residues: 649 sheet: -2.51 (0.45), residues: 129 loop : -2.02 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 2 567 HIS 0.004 0.001 HIS 2 592 PHE 0.030 0.002 PHE 3 195 TYR 0.018 0.002 TYR 2 386 ARG 0.003 0.000 ARG 2 57 *********************** 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 141 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 110 time to evaluate : 1.163 Fit side-chains REVERT: 2 99 LEU cc_start: 0.8254 (OUTLIER) cc_final: 0.7942 (mm) REVERT: 2 438 HIS cc_start: 0.2352 (OUTLIER) cc_final: 0.0811 (t-170) REVERT: 3 256 TYR cc_start: 0.7946 (m-80) cc_final: 0.7622 (m-80) REVERT: 3 275 PHE cc_start: 0.8804 (OUTLIER) cc_final: 0.8402 (t80) REVERT: 3 632 PHE cc_start: 0.8242 (m-80) cc_final: 0.8035 (m-80) REVERT: 3 645 ARG cc_start: 0.6861 (ttt180) cc_final: 0.6518 (ptm160) outliers start: 31 outliers final: 20 residues processed: 133 average time/residue: 0.1978 time to fit residues: 39.7397 Evaluate side-chains 131 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 99 LEU Chi-restraints excluded: chain 2 residue 167 SER 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 438 HIS 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 145 VAL Chi-restraints excluded: chain 3 residue 190 THR Chi-restraints excluded: chain 3 residue 227 ILE Chi-restraints excluded: chain 3 residue 243 THR 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 504 VAL Chi-restraints excluded: chain 3 residue 639 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: 0.5980 chunk 82 optimal weight: 0.6980 chunk 105 optimal weight: 0.0170 chunk 122 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 144 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 0.3980 chunk 66 optimal weight: 20.0000 chunk 89 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11007 Z= 0.182 Angle : 0.554 13.706 15097 Z= 0.276 Chirality : 0.040 0.183 1789 Planarity : 0.004 0.050 1931 Dihedral : 6.181 87.896 2049 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.66 % Allowed : 19.98 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.22), residues: 1488 helix: 0.92 (0.21), residues: 655 sheet: -2.32 (0.47), residues: 119 loop : -1.93 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP 2 567 HIS 0.002 0.000 HIS 2 390 PHE 0.030 0.001 PHE 3 195 TYR 0.013 0.001 TYR 3 434 ARG 0.002 0.000 ARG 2 57 *********************** 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 139 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: 2 202 PHE cc_start: 0.6160 (OUTLIER) cc_final: 0.5815 (m-10) REVERT: 2 388 MET cc_start: 0.7876 (tpp) cc_final: 0.7225 (tpt) REVERT: 3 256 TYR cc_start: 0.7937 (m-80) cc_final: 0.7659 (m-80) REVERT: 3 275 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.8339 (t80) REVERT: 3 310 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7844 (pp) REVERT: 3 645 ARG cc_start: 0.6949 (ttt180) cc_final: 0.6588 (ptm160) outliers start: 25 outliers final: 17 residues processed: 133 average time/residue: 0.1934 time to fit residues: 38.6851 Evaluate side-chains 127 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 1.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 202 PHE Chi-restraints excluded: chain 2 residue 245 MET 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 441 VAL 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 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 454 VAL Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 603 ASN Chi-restraints excluded: chain 3 residue 639 VAL 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: 0.5980 chunk 28 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 131 optimal weight: 8.9990 chunk 138 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3388 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= 0.208 Angle : 0.575 13.297 15097 Z= 0.286 Chirality : 0.041 0.219 1789 Planarity : 0.004 0.049 1931 Dihedral : 6.129 86.226 2049 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 2.76 % Allowed : 20.72 % Favored : 76.51 % 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: -1.02 (0.22), residues: 1488 helix: 0.98 (0.21), residues: 658 sheet: -2.32 (0.44), residues: 130 loop : -2.03 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 2 567 HIS 0.002 0.001 HIS 2 390 PHE 0.029 0.001 PHE 3 195 TYR 0.014 0.002 TYR 2 386 ARG 0.002 0.000 ARG 2 57 *********************** 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 139 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 202 PHE cc_start: 0.6108 (OUTLIER) cc_final: 0.5787 (m-10) REVERT: 2 388 MET cc_start: 0.7864 (tpp) cc_final: 0.7196 (tpt) REVERT: 2 438 HIS cc_start: 0.2397 (OUTLIER) cc_final: 0.1000 (t-170) REVERT: 3 31 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6544 (ptm160) REVERT: 3 256 TYR cc_start: 0.7895 (m-80) cc_final: 0.7590 (m-80) REVERT: 3 275 PHE cc_start: 0.8736 (OUTLIER) cc_final: 0.8413 (t80) REVERT: 3 310 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7806 (pp) REVERT: 3 645 ARG cc_start: 0.6990 (ttt180) cc_final: 0.6671 (ptm160) outliers start: 26 outliers final: 18 residues processed: 133 average time/residue: 0.1931 time to fit residues: 38.6673 Evaluate side-chains 132 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 202 PHE Chi-restraints excluded: chain 2 residue 237 THR 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 438 HIS 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 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 454 VAL Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 603 ASN Chi-restraints excluded: chain 3 residue 639 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 138 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 105 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 121 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 88 optimal weight: 0.4980 chunk 142 optimal weight: 10.0000 chunk 86 optimal weight: 0.0970 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11007 Z= 0.223 Angle : 0.580 14.439 15097 Z= 0.287 Chirality : 0.041 0.247 1789 Planarity : 0.004 0.050 1931 Dihedral : 6.082 83.488 2049 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 2.87 % Allowed : 20.94 % Favored : 76.20 % 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: 1.00 (0.21), residues: 654 sheet: -2.33 (0.44), residues: 130 loop : -1.98 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP 2 567 HIS 0.003 0.001 HIS 2 396 PHE 0.029 0.001 PHE 3 195 TYR 0.014 0.002 TYR 2 386 ARG 0.002 0.000 ARG 2 57 *********************** 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 140 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7749 (mm) REVERT: 2 202 PHE cc_start: 0.6330 (OUTLIER) cc_final: 0.6011 (m-10) REVERT: 2 388 MET cc_start: 0.7872 (tpp) cc_final: 0.7191 (tpt) REVERT: 2 438 HIS cc_start: 0.2397 (OUTLIER) cc_final: 0.0982 (t-170) REVERT: 3 31 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6512 (ptm160) REVERT: 3 256 TYR cc_start: 0.7956 (m-80) cc_final: 0.7633 (m-80) REVERT: 3 275 PHE cc_start: 0.8727 (OUTLIER) cc_final: 0.8409 (t80) REVERT: 3 310 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7767 (pp) REVERT: 3 645 ARG cc_start: 0.7216 (ttt180) cc_final: 0.6959 (ptm160) outliers start: 27 outliers final: 20 residues processed: 133 average time/residue: 0.2002 time to fit residues: 39.9047 Evaluate side-chains 136 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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 237 THR 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 438 HIS 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 227 ILE Chi-restraints excluded: chain 3 residue 243 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 289 SER Chi-restraints excluded: chain 3 residue 310 ILE Chi-restraints excluded: chain 3 residue 454 VAL Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 603 ASN Chi-restraints excluded: chain 3 residue 639 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: 5.9990 chunk 99 optimal weight: 0.6980 chunk 149 optimal weight: 8.9990 chunk 137 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 94 optimal weight: 0.0980 chunk 126 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** 3 386 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11007 Z= 0.362 Angle : 0.645 14.002 15097 Z= 0.324 Chirality : 0.044 0.250 1789 Planarity : 0.004 0.050 1931 Dihedral : 6.203 79.088 2049 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.08 % Allowed : 20.72 % Favored : 76.20 % 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: -1.09 (0.22), residues: 1488 helix: 0.95 (0.21), residues: 651 sheet: -2.65 (0.42), residues: 140 loop : -1.98 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 2 567 HIS 0.004 0.001 HIS 2 390 PHE 0.029 0.002 PHE 3 195 TYR 0.021 0.002 TYR 3 256 ARG 0.004 0.000 ARG 3 68 ********************** 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 140 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: 2 99 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7944 (mm) REVERT: 2 202 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.6069 (m-10) REVERT: 2 438 HIS cc_start: 0.2464 (OUTLIER) cc_final: 0.0737 (t-90) REVERT: 3 31 ARG cc_start: 0.7176 (OUTLIER) cc_final: 0.6550 (ptm160) REVERT: 3 256 TYR cc_start: 0.8047 (m-80) cc_final: 0.7704 (m-80) REVERT: 3 275 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.8456 (t80) REVERT: 3 310 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7796 (pp) REVERT: 3 645 ARG cc_start: 0.7018 (ttt180) cc_final: 0.6767 (ptm160) outliers start: 29 outliers final: 20 residues processed: 130 average time/residue: 0.2118 time to fit residues: 41.1839 Evaluate side-chains 131 residues out of total 1285 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 237 THR Chi-restraints excluded: chain 2 residue 265 VAL Chi-restraints excluded: chain 2 residue 279 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 438 HIS 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 227 ILE Chi-restraints excluded: chain 3 residue 243 THR 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 309 ILE Chi-restraints excluded: chain 3 residue 310 ILE Chi-restraints excluded: chain 3 residue 504 VAL Chi-restraints excluded: chain 3 residue 603 ASN Chi-restraints excluded: chain 3 residue 639 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: 0.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 49 optimal weight: 0.4980 chunk 122 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 86 optimal weight: 0.0670 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 386 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.193565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.178627 restraints weight = 14533.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.175450 restraints weight = 23415.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.173796 restraints weight = 25302.675| |-----------------------------------------------------------------------------| r_work (final): 0.4110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11007 Z= 0.218 Angle : 0.591 14.437 15097 Z= 0.291 Chirality : 0.041 0.251 1789 Planarity : 0.004 0.050 1931 Dihedral : 6.049 77.013 2049 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 2.55 % Allowed : 21.79 % Favored : 75.66 % 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 (0.23), residues: 1488 helix: 1.03 (0.21), residues: 653 sheet: -2.52 (0.43), residues: 130 loop : -1.96 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 2 567 HIS 0.002 0.001 HIS 2 390 PHE 0.028 0.001 PHE 3 195 TYR 0.016 0.002 TYR 2 386 ARG 0.002 0.000 ARG 2 636 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2087.96 seconds wall clock time: 38 minutes 27.87 seconds (2307.87 seconds total)