Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 21:37:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcx_36168/07_2023/8jcx_36168_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcx_36168/07_2023/8jcx_36168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcx_36168/07_2023/8jcx_36168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcx_36168/07_2023/8jcx_36168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcx_36168/07_2023/8jcx_36168_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jcx_36168/07_2023/8jcx_36168_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.040 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 61 5.16 5 C 6674 2.51 5 N 1880 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 ASP 75": "OD1" <-> "OD2" Residue "2 TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ASP 295": "OD1" <-> "OD2" Residue "2 PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 180": "OD1" <-> "OD2" Residue "3 TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 334": "OD1" <-> "OD2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 10617 Number of models: 1 Model: "" Number of chains: 4 Chain: "2" Number of atoms: 5251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 761, 5251 Classifications: {'peptide': 761} Incomplete info: {'truncation_to_alanine': 187} Link IDs: {'PTRANS': 37, 'TRANS': 723} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 701 Unresolved non-hydrogen angles: 902 Unresolved non-hydrogen dihedrals: 581 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 11, 'ASN:plan1': 5, 'TRP:plan': 3, 'ASP:plan': 8, 'PHE:plan': 12, 'GLU:plan': 16, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 387 Chain: "3" Number of atoms: 5286 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 5286 Classifications: {'peptide': 751} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'PTRANS': 29, 'TRANS': 721} Chain breaks: 3 Unresolved non-hydrogen bonds: 692 Unresolved non-hydrogen angles: 879 Unresolved non-hydrogen dihedrals: 574 Unresolved non-hydrogen chiralities: 72 Planarities with less than four sites: {'GLN:plan1': 5, 'ARG:plan': 13, 'TYR:plan': 10, 'ASN:plan1': 10, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 14, 'GLU:plan': 13, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 357 Chain: "2" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'NAG': 1, 'Z99': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.72, per 1000 atoms: 0.54 Number of scatterers: 10617 At special positions: 0 Unit cell: (86.751, 123.165, 183.141, 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 61 16.00 O 2002 8.00 N 1880 7.00 C 6674 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 240 " - pdb=" SG CYS 3 527 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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 Links applied NAG-ASN " NAG 21101 " - " ASN 2 203 " " NAG 31001 " - " ASN 3 209 " Time building additional restraints: 4.60 Conformation dependent library (CDL) restraints added in 1.7 seconds 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 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: 45 helices and 10 sheets defined 43.3% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain '2' and resid 60 through 73 Processing helix chain '2' and resid 95 through 109 removed outlier: 4.051A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N SER 2 109 " --> pdb=" O PHE 2 105 " (cutoff:3.500A) Processing helix chain '2' and resid 145 through 157 removed outlier: 4.269A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 173 No H-bonds generated for 'chain '2' and resid 171 through 173' Processing helix chain '2' and resid 190 through 201 Processing helix chain '2' and resid 220 through 229 Processing helix chain '2' and resid 247 through 259 Processing helix chain '2' and resid 272 through 285 removed outlier: 3.886A pdb=" N ARG 2 276 " --> pdb=" O SER 2 272 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU 2 277 " --> pdb=" O GLU 2 273 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU 2 278 " --> pdb=" O ASP 2 274 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 333 removed outlier: 3.685A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER 2 333 " --> pdb=" O SER 2 329 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 352 Processing helix chain '2' and resid 378 through 399 Processing helix chain '2' and resid 408 through 411 No H-bonds generated for 'chain '2' and resid 408 through 411' Processing helix chain '2' and resid 415 through 421 Processing helix chain '2' and resid 423 through 425 No H-bonds generated for 'chain '2' and resid 423 through 425' 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 568 through 591 Processing helix chain '2' and resid 596 through 600 removed outlier: 3.516A pdb=" N ALA 2 600 " --> pdb=" O PRO 2 596 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 596 through 600' Processing helix chain '2' and resid 603 through 623 Processing helix chain '2' and resid 632 through 659 removed outlier: 4.137A pdb=" N ARG 2 656 " --> pdb=" O THR 2 652 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ILE 2 657 " --> pdb=" O LYS 2 653 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 701 removed outlier: 3.574A pdb=" N VAL 2 680 " --> pdb=" O PRO 2 676 " (cutoff:3.500A) Processing helix chain '2' and resid 724 through 748 removed outlier: 4.042A pdb=" N GLY 2 730 " --> pdb=" O ALA 2 726 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER 2 731 " --> pdb=" O SER 2 727 " (cutoff:3.500A) Processing helix chain '2' and resid 758 through 785 removed outlier: 3.531A pdb=" N CYS 2 770 " --> pdb=" O MET 2 766 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE 2 771 " --> pdb=" O TYR 2 767 " (cutoff:3.500A) Proline residue: 2 778 - end of helix removed outlier: 4.375A pdb=" N SER 2 785 " --> pdb=" O TYR 2 781 " (cutoff:3.500A) Processing helix chain '2' and resid 787 through 817 removed outlier: 3.861A pdb=" N THR 2 792 " --> pdb=" O ARG 2 788 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL 2 805 " --> pdb=" O SER 2 801 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ALA 2 811 " --> pdb=" O GLY 2 807 " (cutoff:3.500A) Proline residue: 2 812 - end of helix Processing helix chain '3' and resid 66 through 81 Processing helix chain '3' and resid 102 through 116 removed outlier: 4.007A pdb=" N LEU 3 110 " --> pdb=" O LEU 3 106 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N PHE 3 112 " --> pdb=" O GLN 3 108 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL 3 113 " --> pdb=" O SER 3 109 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA 3 115 " --> pdb=" O GLU 3 111 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N SER 3 116 " --> pdb=" O PHE 3 112 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 164 removed outlier: 4.256A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N PHE 3 164 " --> pdb=" O LEU 3 160 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 179 No H-bonds generated for 'chain '3' and resid 177 through 179' Processing helix chain '3' and resid 196 through 207 Processing helix chain '3' and resid 221 through 233 Processing helix chain '3' and resid 235 through 237 No H-bonds generated for 'chain '3' and resid 235 through 237' Processing helix chain '3' and resid 253 through 265 Processing helix chain '3' and resid 278 through 289 Processing helix chain '3' and resid 331 through 338 removed outlier: 4.012A pdb=" N ARG 3 335 " --> pdb=" O ARG 3 331 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR 3 336 " --> pdb=" O GLN 3 332 " (cutoff:3.500A) Processing helix chain '3' and resid 351 through 359 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 390 through 411 Processing helix chain '3' and resid 427 through 432 Processing helix chain '3' and resid 494 through 496 No H-bonds generated for 'chain '3' and resid 494 through 496' Processing helix chain '3' and resid 579 through 600 Processing helix chain '3' and resid 614 through 631 removed outlier: 3.945A pdb=" N MET 3 628 " --> pdb=" O LEU 3 624 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) Processing helix chain '3' and resid 640 through 664 removed outlier: 4.436A pdb=" N LEU 3 659 " --> pdb=" O CYS 3 655 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LEU 3 660 " --> pdb=" O TYR 3 656 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N THR 3 661 " --> pdb=" O SER 3 657 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS 3 662 " --> pdb=" O ALA 3 658 " (cutoff:3.500A) Processing helix chain '3' and resid 685 through 705 removed outlier: 3.528A pdb=" N ILE 3 696 " --> pdb=" O CYS 3 692 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL 3 703 " --> pdb=" O GLN 3 699 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER 3 704 " --> pdb=" O ILE 3 700 " (cutoff:3.500A) Processing helix chain '3' and resid 733 through 758 removed outlier: 4.123A pdb=" N ILE 3 739 " --> pdb=" O SER 3 735 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS 3 757 " --> pdb=" O VAL 3 753 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR 3 758 " --> pdb=" O TYR 3 754 " (cutoff:3.500A) Processing helix chain '3' and resid 765 through 790 removed outlier: 3.716A pdb=" N LYS 3 769 " --> pdb=" O PHE 3 765 " (cutoff:3.500A) Proline residue: 3 787 - end of helix removed outlier: 3.558A pdb=" N TYR 3 790 " --> pdb=" O LEU 3 786 " (cutoff:3.500A) Processing helix chain '3' and resid 798 through 824 removed outlier: 3.511A pdb=" N MET 3 803 " --> pdb=" O GLN 3 799 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing sheet with id= A, first strand: chain '2' and resid 84 through 90 removed outlier: 6.857A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N GLY 2 35 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL 2 139 " --> pdb=" O GLY 2 35 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU 2 37 " --> pdb=" O VAL 2 139 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLY 2 141 " --> pdb=" O LEU 2 37 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 162 through 164 Processing sheet with id= C, first strand: chain '2' and resid 210 through 212 removed outlier: 6.204A pdb=" N GLU 2 239 " --> pdb=" O ALA 2 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain '2' and resid 266 through 268 Processing sheet with id= E, first strand: chain '2' and resid 315 through 319 removed outlier: 6.274A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU 2 459 " --> pdb=" O TYR 2 468 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TYR 2 468 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 32 through 35 removed outlier: 6.302A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLY 3 42 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N VAL 3 145 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU 3 44 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N GLY 3 147 " --> pdb=" O LEU 3 44 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N GLY 3 147 " --> pdb=" O PRO 3 167 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ILE 3 169 " --> pdb=" O GLY 3 147 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 240 through 242 removed outlier: 3.647A pdb=" N VAL 3 213 " --> pdb=" O CYS 3 240 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR 3 215 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N VAL 3 271 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR 3 296 " --> pdb=" O VAL 3 272 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LEU 3 274 " --> pdb=" O THR 3 296 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL 3 298 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '3' and resid 320 through 325 removed outlier: 3.872A pdb=" N ALA 3 320 " --> pdb=" O PHE 3 471 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain '3' and resid 472 through 474 Processing sheet with id= J, first strand: chain '3' and resid 518 through 521 removed outlier: 3.770A pdb=" N ILE 3 532 " --> pdb=" O LYS 3 519 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N MET 3 521 " --> pdb=" O ILE 3 530 " (cutoff:3.500A) 467 hydrogen bonds defined for protein. 1386 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: 3.18 Time building geometry restraints manager: 4.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3609 1.34 - 1.46: 2523 1.46 - 1.58: 4630 1.58 - 1.70: 3 1.70 - 1.81: 77 Bond restraints: 10842 Sorted by residual: bond pdb=" CAT Z99 31002 " pdb=" OAP Z99 31002 " ideal model delta sigma weight residual 1.364 1.453 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" CAT Z99 21102 " pdb=" OAP Z99 21102 " ideal model delta sigma weight residual 1.364 1.452 -0.088 2.00e-02 2.50e+03 1.95e+01 bond pdb=" CAS Z99 31002 " pdb=" OAP Z99 31002 " ideal model delta sigma weight residual 1.369 1.449 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" CAS Z99 21102 " pdb=" OAP Z99 21102 " ideal model delta sigma weight residual 1.369 1.448 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" CB PRO 2 496 " pdb=" CG PRO 2 496 " ideal model delta sigma weight residual 1.492 1.620 -0.128 5.00e-02 4.00e+02 6.58e+00 ... (remaining 10837 not shown) Histogram of bond angle deviations from ideal: 59.72 - 74.57: 6 74.57 - 89.43: 0 89.43 - 104.28: 163 104.28 - 119.13: 8643 119.13 - 133.99: 6023 Bond angle restraints: 14835 Sorted by residual: angle pdb=" CA PRO 2 496 " pdb=" N PRO 2 496 " pdb=" CD PRO 2 496 " ideal model delta sigma weight residual 112.00 104.96 7.04 1.40e+00 5.10e-01 2.53e+01 angle pdb=" CA PRO 3 267 " pdb=" N PRO 3 267 " pdb=" CD PRO 3 267 " ideal model delta sigma weight residual 112.00 106.14 5.86 1.40e+00 5.10e-01 1.75e+01 angle pdb=" CA PRO 2 133 " pdb=" N PRO 2 133 " pdb=" CD PRO 2 133 " ideal model delta sigma weight residual 112.00 106.21 5.79 1.40e+00 5.10e-01 1.71e+01 angle pdb=" CAX Z99 31002 " pdb=" CAZ Z99 31002 " pdb=" CAY Z99 31002 " ideal model delta sigma weight residual 120.67 110.99 9.68 3.00e+00 1.11e-01 1.04e+01 angle pdb=" OAC Z99 31002 " pdb=" CAR Z99 31002 " pdb=" OAE Z99 31002 " ideal model delta sigma weight residual 127.15 119.14 8.01 3.00e+00 1.11e-01 7.13e+00 ... (remaining 14830 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 6011 17.66 - 35.33: 325 35.33 - 52.99: 60 52.99 - 70.66: 7 70.66 - 88.32: 6 Dihedral angle restraints: 6409 sinusoidal: 2027 harmonic: 4382 Sorted by residual: dihedral pdb=" CB CYS 3 57 " pdb=" SG CYS 3 57 " pdb=" SG CYS 3 99 " pdb=" CB CYS 3 99 " ideal model delta sinusoidal sigma weight residual 93.00 27.53 65.47 1 1.00e+01 1.00e-02 5.61e+01 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 93.00 147.49 -54.49 1 1.00e+01 1.00e-02 4.02e+01 dihedral pdb=" CB CYS 2 500 " pdb=" SG CYS 2 500 " pdb=" SG CYS 2 519 " pdb=" CB CYS 2 519 " ideal model delta sinusoidal sigma weight residual -86.00 -36.85 -49.15 1 1.00e+01 1.00e-02 3.32e+01 ... (remaining 6406 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.050: 1718 1.050 - 2.100: 0 2.100 - 3.150: 0 3.150 - 4.200: 0 4.200 - 5.250: 2 Chirality restraints: 1720 Sorted by residual: chirality pdb=" CAW Z99 21102 " pdb=" CAN Z99 21102 " pdb=" CAU Z99 21102 " pdb=" CAV Z99 21102 " both_signs ideal model delta sigma weight residual False 2.61 -2.64 5.25 2.00e-01 2.50e+01 6.89e+02 chirality pdb=" CAW Z99 31002 " pdb=" CAN Z99 31002 " pdb=" CAU Z99 31002 " pdb=" CAV Z99 31002 " both_signs ideal model delta sigma weight residual False 2.61 -2.52 5.13 2.00e-01 2.50e+01 6.57e+02 chirality pdb=" CAZ Z99 21102 " pdb=" CAO Z99 21102 " pdb=" CAX Z99 21102 " pdb=" CAY Z99 21102 " both_signs ideal model delta sigma weight residual True 2.39 -2.71 -0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 1717 not shown) Planarity restraints: 1959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA 2 132 " -0.071 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO 2 133 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO 2 133 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO 2 133 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 2 495 " 0.052 5.00e-02 4.00e+02 7.47e-02 8.92e+00 pdb=" N PRO 2 496 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO 2 496 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 2 496 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS 3 266 " 0.034 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO 3 267 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO 3 267 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO 3 267 " 0.027 5.00e-02 4.00e+02 ... (remaining 1956 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1715 2.76 - 3.30: 10121 3.30 - 3.83: 17895 3.83 - 4.37: 19356 4.37 - 4.90: 34386 Nonbonded interactions: 83473 Sorted by model distance: nonbonded pdb=" OE1 GLN 2 159 " pdb=" OH TYR 2 180 " model vdw 2.225 2.440 nonbonded pdb=" NH1 ARG 2 460 " pdb=" O ALA 2 461 " model vdw 2.269 2.520 nonbonded pdb=" O ILE 3 788 " pdb=" OG1 THR 3 792 " model vdw 2.271 2.440 nonbonded pdb=" NH1 ARG 3 31 " pdb=" OD2 ASP 3 353 " model vdw 2.297 2.520 nonbonded pdb=" NE1 TRP 2 204 " pdb=" O LEU 2 495 " model vdw 2.304 2.520 ... (remaining 83468 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.370 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: 11.050 Check model and map are aligned: 0.170 Set scattering table: 0.130 Process input model: 29.700 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:10.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 : 0.003 0.128 10842 Z= 0.239 Angle : 0.532 9.675 14835 Z= 0.259 Chirality : 0.182 5.250 1720 Planarity : 0.004 0.104 1957 Dihedral : 11.267 88.322 3517 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.35 (0.23), residues: 1498 helix: 2.58 (0.21), residues: 648 sheet: -2.03 (0.45), residues: 147 loop : -1.62 (0.23), residues: 703 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 1.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 1.0437 time to fit residues: 148.1750 Evaluate side-chains 101 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.1980 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 61 optimal weight: 40.0000 chunk 118 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 71 optimal weight: 40.0000 chunk 88 optimal weight: 0.1980 chunk 137 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 268 ASN 3 345 ASN 3 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 10842 Z= 0.229 Angle : 0.534 11.265 14835 Z= 0.262 Chirality : 0.042 0.204 1720 Planarity : 0.003 0.057 1957 Dihedral : 4.005 58.756 1614 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer Outliers : 2.08 % 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: 0.35 (0.23), residues: 1498 helix: 2.56 (0.20), residues: 642 sheet: -1.76 (0.43), residues: 148 loop : -1.63 (0.23), residues: 708 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.201 Fit side-chains outliers start: 19 outliers final: 5 residues processed: 112 average time/residue: 0.9361 time to fit residues: 116.3744 Evaluate side-chains 104 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.198 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 0.1599 time to fit residues: 2.2911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 137 optimal weight: 9.9990 chunk 148 optimal weight: 0.0000 chunk 122 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 48 ASN 3 156 GLN 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 10842 Z= 0.302 Angle : 0.559 10.420 14835 Z= 0.282 Chirality : 0.044 0.224 1720 Planarity : 0.004 0.060 1957 Dihedral : 4.238 51.935 1614 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 2.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.22), residues: 1498 helix: 2.37 (0.20), residues: 643 sheet: -1.86 (0.42), residues: 150 loop : -1.67 (0.22), residues: 705 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 98 time to evaluate : 1.139 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 6 residues processed: 114 average time/residue: 0.9357 time to fit residues: 118.1539 Evaluate side-chains 100 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 1.5544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 71 optimal weight: 30.0000 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 145 optimal weight: 30.0000 chunk 72 optimal weight: 40.0000 chunk 130 optimal weight: 9.9990 chunk 39 optimal weight: 0.0010 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 10842 Z= 0.237 Angle : 0.509 8.765 14835 Z= 0.257 Chirality : 0.042 0.222 1720 Planarity : 0.003 0.057 1957 Dihedral : 3.978 32.091 1614 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 2.63 % 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: 0.20 (0.22), residues: 1498 helix: 2.41 (0.20), residues: 643 sheet: -1.81 (0.43), residues: 150 loop : -1.69 (0.22), residues: 705 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 94 time to evaluate : 1.207 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 108 average time/residue: 0.9458 time to fit residues: 114.3965 Evaluate side-chains 102 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 3 average time/residue: 0.2607 time to fit residues: 2.7596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 2 optimal weight: 0.0370 chunk 108 optimal weight: 0.0060 chunk 60 optimal weight: 9.9990 chunk 124 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 74 optimal weight: 40.0000 chunk 131 optimal weight: 50.0000 chunk 36 optimal weight: 1.9990 overall best weight: 0.7676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 10842 Z= 0.250 Angle : 0.507 8.415 14835 Z= 0.258 Chirality : 0.042 0.227 1720 Planarity : 0.003 0.055 1957 Dihedral : 3.897 20.234 1614 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer Outliers : 2.63 % 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: 0.20 (0.22), residues: 1498 helix: 2.41 (0.20), residues: 643 sheet: -1.78 (0.42), residues: 150 loop : -1.70 (0.22), residues: 705 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 93 time to evaluate : 1.131 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 108 average time/residue: 0.8288 time to fit residues: 100.7166 Evaluate side-chains 105 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.158 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1672 time to fit residues: 2.3870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 10.0000 chunk 131 optimal weight: 50.0000 chunk 28 optimal weight: 0.3980 chunk 85 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 146 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 12 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.047 10842 Z= 0.373 Angle : 0.576 8.546 14835 Z= 0.295 Chirality : 0.045 0.231 1720 Planarity : 0.004 0.052 1957 Dihedral : 4.175 21.247 1614 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer Outliers : 3.18 % 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: 0.05 (0.22), residues: 1498 helix: 2.27 (0.20), residues: 641 sheet: -1.86 (0.42), residues: 150 loop : -1.74 (0.22), residues: 707 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 94 time to evaluate : 1.101 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 114 average time/residue: 0.8458 time to fit residues: 108.0284 Evaluate side-chains 103 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 87 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 13 residues processed: 3 average time/residue: 0.1638 time to fit residues: 2.2658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 40.0000 chunk 16 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 82 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 145 optimal weight: 30.0000 chunk 91 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 10842 Z= 0.223 Angle : 0.505 9.162 14835 Z= 0.259 Chirality : 0.042 0.245 1720 Planarity : 0.003 0.051 1957 Dihedral : 3.968 20.656 1614 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer Outliers : 3.18 % 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: 0.14 (0.22), residues: 1498 helix: 2.36 (0.20), residues: 645 sheet: -1.82 (0.42), residues: 150 loop : -1.74 (0.22), residues: 703 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 95 time to evaluate : 1.099 Fit side-chains revert: symmetry clash outliers start: 29 outliers final: 15 residues processed: 116 average time/residue: 0.8843 time to fit residues: 114.5262 Evaluate side-chains 110 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 13 residues processed: 2 average time/residue: 0.7039 time to fit residues: 3.1933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.0470 chunk 58 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.0020 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 71 optimal weight: 30.0000 chunk 13 optimal weight: 0.5980 chunk 114 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 overall best weight: 0.5086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 10842 Z= 0.194 Angle : 0.497 9.975 14835 Z= 0.254 Chirality : 0.042 0.254 1720 Planarity : 0.003 0.051 1957 Dihedral : 3.867 20.491 1614 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.22), residues: 1498 helix: 2.44 (0.21), residues: 644 sheet: -1.79 (0.42), residues: 150 loop : -1.70 (0.22), residues: 704 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.164 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 109 average time/residue: 0.8690 time to fit residues: 106.7119 Evaluate side-chains 104 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 14 residues processed: 2 average time/residue: 0.2422 time to fit residues: 2.1336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 89 optimal weight: 0.1980 chunk 143 optimal weight: 4.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 10842 Z= 0.254 Angle : 0.525 10.613 14835 Z= 0.267 Chirality : 0.043 0.265 1720 Planarity : 0.003 0.050 1957 Dihedral : 3.945 20.574 1614 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer Outliers : 2.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.22), residues: 1498 helix: 2.41 (0.21), residues: 644 sheet: -1.76 (0.42), residues: 150 loop : -1.71 (0.22), residues: 704 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 1.211 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 13 residues processed: 110 average time/residue: 0.8964 time to fit residues: 110.6853 Evaluate side-chains 105 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.177 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1023 time to fit residues: 1.8559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 30.0000 chunk 99 optimal weight: 0.5980 chunk 150 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 92 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 127 optimal weight: 10.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 10842 Z= 0.235 Angle : 0.522 11.062 14835 Z= 0.266 Chirality : 0.042 0.260 1720 Planarity : 0.003 0.050 1957 Dihedral : 3.952 20.402 1614 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1498 helix: 2.43 (0.21), residues: 644 sheet: -1.86 (0.41), residues: 155 loop : -1.65 (0.22), residues: 699 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2996 Ramachandran restraints generated. 1498 Oldfield, 0 Emsley, 1498 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 1.109 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 105 average time/residue: 0.9004 time to fit residues: 106.0635 Evaluate side-chains 101 residues out of total 1284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 1.169 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 1.6478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 123 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 105 optimal weight: 0.1980 chunk 6 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 268 ASN 3 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.226162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.130733 restraints weight = 11009.808| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.78 r_work: 0.3271 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 10842 Z= 0.205 Angle : 0.509 11.008 14835 Z= 0.259 Chirality : 0.042 0.258 1720 Planarity : 0.003 0.049 1957 Dihedral : 3.888 20.453 1614 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer Outliers : 1.86 % Cbeta Deviations : 0.07 % 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: 0.28 (0.23), residues: 1498 helix: 2.48 (0.21), residues: 644 sheet: -1.84 (0.42), residues: 155 loop : -1.63 (0.23), residues: 699 =============================================================================== Job complete usr+sys time: 3032.08 seconds wall clock time: 54 minutes 55.83 seconds (3295.83 seconds total)