Starting phenix.real_space_refine on Wed Mar 20 00:39:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwb_35052/03_2024/8hwb_35052_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwb_35052/03_2024/8hwb_35052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwb_35052/03_2024/8hwb_35052.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwb_35052/03_2024/8hwb_35052.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwb_35052/03_2024/8hwb_35052_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwb_35052/03_2024/8hwb_35052_updated.pdb" } resolution = 3.9 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= 0.002 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: 6 Type Number sf(0) Gaussians P 23 5.49 5 Mg 4 5.21 5 S 144 5.16 5 C 16283 2.51 5 N 4370 2.21 5 O 4916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 335": "OD1" <-> "OD2" Residue "A GLU 360": "OE1" <-> "OE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A GLU 382": "OE1" <-> "OE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A GLU 504": "OE1" <-> "OE2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B GLU 405": "OE1" <-> "OE2" Residue "B GLU 474": "OE1" <-> "OE2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B GLU 483": "OE1" <-> "OE2" Residue "B GLU 526": "OE1" <-> "OE2" Residue "B PHE 626": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 343": "OE1" <-> "OE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C GLU 480": "OE1" <-> "OE2" Residue "C PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 39": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D GLU 60": "OE1" <-> "OE2" Residue "D TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 237": "OE1" <-> "OE2" Residue "D GLU 244": "OE1" <-> "OE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "E GLU 49": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 156": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E GLU 228": "OE1" <-> "OE2" Residue "E GLU 237": "OE1" <-> "OE2" Residue "E GLU 382": "OE1" <-> "OE2" Residue "E GLU 474": "OE1" <-> "OE2" Residue "E GLU 691": "OE1" <-> "OE2" Residue "E GLU 692": "OE1" <-> "OE2" Residue "F GLU 343": "OE1" <-> "OE2" Residue "F GLU 360": "OE1" <-> "OE2" Residue "F GLU 382": "OE1" <-> "OE2" Residue "F GLU 393": "OE1" <-> "OE2" Residue "F GLU 474": "OE1" <-> "OE2" Residue "K GLU 33": "OE1" <-> "OE2" Residue "K GLU 49": "OE1" <-> "OE2" Residue "K GLU 59": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K GLU 205": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25740 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "B" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "C" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "D" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "E" Number of atoms: 5659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 700, 5659 Classifications: {'peptide': 700} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 667} Chain: "F" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3060 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 18, 'TRANS': 360} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "K" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1876 Classifications: {'peptide': 231} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 223} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.43, per 1000 atoms: 0.52 Number of scatterers: 25740 At special positions: 0 Unit cell: (130.305, 127.02, 175.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 144 16.00 P 23 15.00 Mg 4 11.99 O 4916 8.00 N 4370 7.00 C 16283 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 9.68 Conformation dependent library (CDL) restraints added in 4.7 seconds 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 133 helices and 38 sheets defined 35.6% alpha, 9.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.29 Creating SS restraints... Processing helix chain 'A' and resid 326 through 336 Processing helix chain 'A' and resid 364 through 374 removed outlier: 5.099A pdb=" N HIS A 373 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLN A 374 " --> pdb=" O SER A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 448 through 450 No H-bonds generated for 'chain 'A' and resid 448 through 450' Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 477 through 490 removed outlier: 3.875A pdb=" N CYS A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 520 Processing helix chain 'A' and resid 529 through 531 No H-bonds generated for 'chain 'A' and resid 529 through 531' Processing helix chain 'A' and resid 542 through 547 removed outlier: 4.685A pdb=" N MET A 547 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 633 through 640 removed outlier: 4.636A pdb=" N GLU A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 659 removed outlier: 4.106A pdb=" N GLY A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 694 through 699 Processing helix chain 'B' and resid 326 through 335 Processing helix chain 'B' and resid 364 through 374 removed outlier: 4.823A pdb=" N HIS B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLN B 374 " --> pdb=" O SER B 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 removed outlier: 3.825A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 383 " --> pdb=" O TYR B 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 383' Processing helix chain 'B' and resid 386 through 398 Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 448 through 450 No H-bonds generated for 'chain 'B' and resid 448 through 450' Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 476 through 489 removed outlier: 3.963A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 542 through 547 removed outlier: 4.790A pdb=" N MET B 547 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 615 through 618 No H-bonds generated for 'chain 'B' and resid 615 through 618' Processing helix chain 'B' and resid 633 through 640 removed outlier: 3.623A pdb=" N ARG B 636 " --> pdb=" O PRO B 633 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N GLU B 637 " --> pdb=" O SER B 634 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA B 638 " --> pdb=" O GLY B 635 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 659 removed outlier: 3.955A pdb=" N GLY B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 679 Processing helix chain 'B' and resid 694 through 699 removed outlier: 3.592A pdb=" N TYR B 699 " --> pdb=" O ASP B 695 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 335 Processing helix chain 'C' and resid 364 through 374 removed outlier: 5.232A pdb=" N HIS C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N GLN C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.703A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 382' Processing helix chain 'C' and resid 386 through 398 Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 456 through 468 Processing helix chain 'C' and resid 476 through 489 removed outlier: 3.900A pdb=" N CYS C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 529 through 531 No H-bonds generated for 'chain 'C' and resid 529 through 531' Processing helix chain 'C' and resid 542 through 547 removed outlier: 4.734A pdb=" N MET C 547 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 578 removed outlier: 3.722A pdb=" N THR C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 618 No H-bonds generated for 'chain 'C' and resid 615 through 618' Processing helix chain 'C' and resid 633 through 640 removed outlier: 3.860A pdb=" N ARG C 636 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLU C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 659 Processing helix chain 'C' and resid 665 through 679 Processing helix chain 'C' and resid 690 through 692 No H-bonds generated for 'chain 'C' and resid 690 through 692' Processing helix chain 'C' and resid 694 through 698 Processing helix chain 'D' and resid 3 through 6 No H-bonds generated for 'chain 'D' and resid 3 through 6' Processing helix chain 'D' and resid 21 through 24 No H-bonds generated for 'chain 'D' and resid 21 through 24' Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.560A pdb=" N ASP D 45 " --> pdb=" O GLU D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 104 removed outlier: 3.504A pdb=" N GLN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 144 through 159 removed outlier: 4.450A pdb=" N ARG D 152 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 168 Processing helix chain 'D' and resid 204 through 207 Processing helix chain 'D' and resid 227 through 230 No H-bonds generated for 'chain 'D' and resid 227 through 230' Processing helix chain 'D' and resid 243 through 253 Processing helix chain 'D' and resid 261 through 263 No H-bonds generated for 'chain 'D' and resid 261 through 263' Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'D' and resid 326 through 335 Processing helix chain 'D' and resid 364 through 374 removed outlier: 5.012A pdb=" N HIS D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLN D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 386 through 398 removed outlier: 3.514A pdb=" N ASP D 398 " --> pdb=" O ALA D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 434 No H-bonds generated for 'chain 'D' and resid 432 through 434' Processing helix chain 'D' and resid 456 through 468 Processing helix chain 'D' and resid 473 through 489 removed outlier: 3.627A pdb=" N LYS D 476 " --> pdb=" O ASP D 473 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N LYS D 477 " --> pdb=" O GLU D 474 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ASN D 478 " --> pdb=" O ASN D 475 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N CYS D 489 " --> pdb=" O LEU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 520 Processing helix chain 'D' and resid 529 through 531 No H-bonds generated for 'chain 'D' and resid 529 through 531' Processing helix chain 'D' and resid 542 through 547 removed outlier: 4.236A pdb=" N MET D 547 " --> pdb=" O PHE D 543 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 577 Processing helix chain 'D' and resid 615 through 620 removed outlier: 3.621A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ARG D 620 " --> pdb=" O ALA D 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 615 through 620' Processing helix chain 'D' and resid 633 through 640 removed outlier: 3.522A pdb=" N ARG D 636 " --> pdb=" O PRO D 633 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLU D 637 " --> pdb=" O SER D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 655 through 658 No H-bonds generated for 'chain 'D' and resid 655 through 658' Processing helix chain 'D' and resid 665 through 679 Processing helix chain 'D' and resid 690 through 692 No H-bonds generated for 'chain 'D' and resid 690 through 692' Processing helix chain 'D' and resid 694 through 699 removed outlier: 3.816A pdb=" N TYR D 699 " --> pdb=" O ASP D 695 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 6 No H-bonds generated for 'chain 'E' and resid 3 through 6' Processing helix chain 'E' and resid 21 through 24 No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 37 through 46 Processing helix chain 'E' and resid 79 through 104 Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 144 through 159 removed outlier: 5.042A pdb=" N ARG E 152 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N THR E 153 " --> pdb=" O ALA E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 168 Processing helix chain 'E' and resid 204 through 207 Processing helix chain 'E' and resid 227 through 229 No H-bonds generated for 'chain 'E' and resid 227 through 229' Processing helix chain 'E' and resid 243 through 253 removed outlier: 3.561A pdb=" N ILE E 253 " --> pdb=" O ARG E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 313 No H-bonds generated for 'chain 'E' and resid 311 through 313' Processing helix chain 'E' and resid 326 through 335 Processing helix chain 'E' and resid 364 through 374 removed outlier: 5.032A pdb=" N HIS E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLN E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 383 removed outlier: 3.942A pdb=" N SER E 381 " --> pdb=" O LYS E 377 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLU E 382 " --> pdb=" O GLU E 378 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU E 383 " --> pdb=" O TYR E 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 383' Processing helix chain 'E' and resid 386 through 397 Processing helix chain 'E' and resid 432 through 434 No H-bonds generated for 'chain 'E' and resid 432 through 434' Processing helix chain 'E' and resid 448 through 450 No H-bonds generated for 'chain 'E' and resid 448 through 450' Processing helix chain 'E' and resid 456 through 468 Processing helix chain 'E' and resid 473 through 489 removed outlier: 3.776A pdb=" N LYS E 476 " --> pdb=" O ASP E 473 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N LYS E 477 " --> pdb=" O GLU E 474 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN E 478 " --> pdb=" O ASN E 475 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER E 488 " --> pdb=" O THR E 485 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 520 Processing helix chain 'E' and resid 529 through 532 Processing helix chain 'E' and resid 542 through 547 removed outlier: 4.012A pdb=" N MET E 547 " --> pdb=" O PHE E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 576 Processing helix chain 'E' and resid 633 through 641 removed outlier: 5.186A pdb=" N GLU E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 658 No H-bonds generated for 'chain 'E' and resid 655 through 658' Processing helix chain 'E' and resid 665 through 679 Processing helix chain 'E' and resid 690 through 692 No H-bonds generated for 'chain 'E' and resid 690 through 692' Processing helix chain 'E' and resid 694 through 699 removed outlier: 4.251A pdb=" N TYR E 699 " --> pdb=" O ASP E 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 335 Processing helix chain 'F' and resid 364 through 374 removed outlier: 5.012A pdb=" N HIS F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N GLN F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 382 removed outlier: 4.565A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 377 through 382' Processing helix chain 'F' and resid 386 through 398 removed outlier: 3.516A pdb=" N ASP F 398 " --> pdb=" O ALA F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 433 Processing helix chain 'F' and resid 456 through 468 Processing helix chain 'F' and resid 473 through 489 removed outlier: 3.660A pdb=" N LYS F 476 " --> pdb=" O ASP F 473 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS F 477 " --> pdb=" O GLU F 474 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN F 478 " --> pdb=" O ASN F 475 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LEU F 486 " --> pdb=" O GLU F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 520 Processing helix chain 'F' and resid 529 through 531 No H-bonds generated for 'chain 'F' and resid 529 through 531' Processing helix chain 'F' and resid 571 through 576 Processing helix chain 'F' and resid 615 through 620 removed outlier: 4.589A pdb=" N ARG F 620 " --> pdb=" O ALA F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 633 through 640 removed outlier: 5.113A pdb=" N GLU F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 655 through 658 No H-bonds generated for 'chain 'F' and resid 655 through 658' Processing helix chain 'F' and resid 665 through 679 Processing helix chain 'F' and resid 690 through 692 No H-bonds generated for 'chain 'F' and resid 690 through 692' Processing helix chain 'F' and resid 694 through 698 Processing helix chain 'K' and resid 4 through 6 No H-bonds generated for 'chain 'K' and resid 4 through 6' Processing helix chain 'K' and resid 21 through 25 Processing helix chain 'K' and resid 37 through 46 Processing helix chain 'K' and resid 79 through 103 removed outlier: 3.508A pdb=" N ASP K 88 " --> pdb=" O THR K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 109 through 118 removed outlier: 3.506A pdb=" N ILE K 113 " --> pdb=" O HIS K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 159 removed outlier: 4.751A pdb=" N ARG K 152 " --> pdb=" O ILE K 148 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N THR K 153 " --> pdb=" O ALA K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 167 No H-bonds generated for 'chain 'K' and resid 164 through 167' Processing helix chain 'K' and resid 204 through 207 Processing sheet with id= A, first strand: chain 'A' and resid 412 through 415 removed outlier: 3.657A pdb=" N GLY A 418 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 622 through 626 removed outlier: 3.504A pdb=" N ASP A 603 " --> pdb=" O CYS A 555 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 629 through 631 Processing sheet with id= D, first strand: chain 'B' and resid 339 through 341 Processing sheet with id= E, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.961A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 621 through 626 removed outlier: 6.063A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VAL B 553 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ASP B 603 " --> pdb=" O VAL B 553 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N CYS B 555 " --> pdb=" O ASP B 603 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 581 through 583 Processing sheet with id= H, first strand: chain 'B' and resid 629 through 631 Processing sheet with id= I, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.916A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 621 through 626 removed outlier: 5.959A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL C 553 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 581 through 583 Processing sheet with id= L, first strand: chain 'C' and resid 629 through 631 Processing sheet with id= M, first strand: chain 'D' and resid 32 through 35 removed outlier: 4.744A pdb=" N PHE D 12 " --> pdb=" O SER D 55 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 120 through 122 removed outlier: 4.110A pdb=" N ILE D 67 " --> pdb=" O PHE D 137 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP D 139 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 11.026A pdb=" N VAL D 65 " --> pdb=" O ASP D 139 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 123 through 125 Processing sheet with id= P, first strand: chain 'D' and resid 294 through 299 removed outlier: 3.694A pdb=" N LYS D 317 " --> pdb=" O ILE D 305 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 339 through 341 Processing sheet with id= R, first strand: chain 'D' and resid 412 through 415 removed outlier: 4.002A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 621 through 626 removed outlier: 5.654A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 581 through 583 Processing sheet with id= U, first strand: chain 'D' and resid 629 through 631 Processing sheet with id= V, first strand: chain 'E' and resid 11 through 14 removed outlier: 3.557A pdb=" N GLU E 33 " --> pdb=" O VAL E 13 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= X, first strand: chain 'E' and resid 64 through 66 Processing sheet with id= Y, first strand: chain 'E' and resid 68 through 73 Processing sheet with id= Z, first strand: chain 'E' and resid 302 through 305 Processing sheet with id= AA, first strand: chain 'E' and resid 339 through 341 removed outlier: 3.520A pdb=" N LYS E 356 " --> pdb=" O VAL E 349 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE E 351 " --> pdb=" O SER E 354 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 412 through 415 removed outlier: 3.644A pdb=" N GLY E 418 " --> pdb=" O PHE E 415 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 621 through 625 removed outlier: 5.864A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE E 600 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE E 501 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE E 602 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 581 through 583 Processing sheet with id= AE, first strand: chain 'E' and resid 629 through 631 Processing sheet with id= AF, first strand: chain 'F' and resid 412 through 415 Processing sheet with id= AG, first strand: chain 'F' and resid 621 through 626 removed outlier: 6.213A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE F 600 " --> pdb=" O THR F 499 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N PHE F 501 " --> pdb=" O ILE F 600 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE F 602 " --> pdb=" O PHE F 501 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N GLY F 503 " --> pdb=" O ILE F 602 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL F 553 " --> pdb=" O ILE F 601 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ASP F 603 " --> pdb=" O VAL F 553 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N CYS F 555 " --> pdb=" O ASP F 603 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'F' and resid 628 through 631 removed outlier: 7.367A pdb=" N LYS F 647 " --> pdb=" O HIS F 629 " (cutoff:3.500A) removed outlier: 8.498A pdb=" N SER F 631 " --> pdb=" O LYS F 647 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N LYS F 649 " --> pdb=" O SER F 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'K' and resid 11 through 14 removed outlier: 3.553A pdb=" N VAL K 13 " --> pdb=" O GLU K 33 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU K 33 " --> pdb=" O VAL K 13 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AK, first strand: chain 'K' and resid 71 through 73 removed outlier: 3.544A pdb=" N PHE K 133 " --> pdb=" O VAL K 71 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'K' and resid 64 through 68 removed outlier: 7.099A pdb=" N THR K 140 " --> pdb=" O ILE K 67 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 1827 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: 9.35 Time building geometry restraints manager: 10.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6639 1.33 - 1.45: 4767 1.45 - 1.58: 14628 1.58 - 1.70: 40 1.70 - 1.82: 207 Bond restraints: 26281 Sorted by residual: bond pdb=" C GLU D 237 " pdb=" N PRO D 238 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.26e-02 6.30e+03 6.07e+00 bond pdb=" N LEU A 577 " pdb=" CA LEU A 577 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.35e-02 5.49e+03 6.03e+00 bond pdb=" N LEU E 321 " pdb=" CA LEU E 321 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.51e+00 bond pdb=" N SER K 160 " pdb=" CA SER K 160 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.50e+00 bond pdb=" N LEU C 700 " pdb=" CA LEU C 700 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.45e+00 ... (remaining 26276 not shown) Histogram of bond angle deviations from ideal: 99.38 - 107.47: 964 107.47 - 115.56: 16129 115.56 - 123.64: 17880 123.64 - 131.73: 582 131.73 - 139.82: 38 Bond angle restraints: 35593 Sorted by residual: angle pdb=" CA PRO E 29 " pdb=" N PRO E 29 " pdb=" CD PRO E 29 " ideal model delta sigma weight residual 112.00 106.09 5.91 1.40e+00 5.10e-01 1.78e+01 angle pdb=" N LEU F 700 " pdb=" CA LEU F 700 " pdb=" C LEU F 700 " ideal model delta sigma weight residual 113.50 108.43 5.07 1.23e+00 6.61e-01 1.70e+01 angle pdb=" CA GLU D 382 " pdb=" CB GLU D 382 " pdb=" CG GLU D 382 " ideal model delta sigma weight residual 114.10 122.19 -8.09 2.00e+00 2.50e-01 1.63e+01 angle pdb=" N PHE B 698 " pdb=" CA PHE B 698 " pdb=" C PHE B 698 " ideal model delta sigma weight residual 112.23 107.20 5.03 1.26e+00 6.30e-01 1.60e+01 angle pdb=" N MET F 458 " pdb=" CA MET F 458 " pdb=" CB MET F 458 " ideal model delta sigma weight residual 110.01 115.80 -5.79 1.45e+00 4.76e-01 1.59e+01 ... (remaining 35588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 15412 31.41 - 62.82: 670 62.82 - 94.23: 44 94.23 - 125.64: 1 125.64 - 157.05: 2 Dihedral angle restraints: 16129 sinusoidal: 6838 harmonic: 9291 Sorted by residual: dihedral pdb=" C4' DT S 3 " pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " pdb=" P DT S 4 " ideal model delta sinusoidal sigma weight residual 220.00 62.95 157.05 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DT S 2 " pdb=" C3' DT S 2 " pdb=" O3' DT S 2 " pdb=" P DT S 3 " ideal model delta sinusoidal sigma weight residual 220.00 67.88 152.12 1 3.50e+01 8.16e-04 1.48e+01 dihedral pdb=" CA ASP A 335 " pdb=" CB ASP A 335 " pdb=" CG ASP A 335 " pdb=" OD1 ASP A 335 " ideal model delta sinusoidal sigma weight residual -30.00 -90.06 60.06 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 16126 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2683 0.038 - 0.076: 949 0.076 - 0.113: 313 0.113 - 0.151: 34 0.151 - 0.189: 5 Chirality restraints: 3984 Sorted by residual: chirality pdb=" CA LEU A 700 " pdb=" N LEU A 700 " pdb=" C LEU A 700 " pdb=" CB LEU A 700 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.91e-01 chirality pdb=" CB ILE A 681 " pdb=" CA ILE A 681 " pdb=" CG1 ILE A 681 " pdb=" CG2 ILE A 681 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.46e-01 chirality pdb=" CA LEU A 577 " pdb=" N LEU A 577 " pdb=" C LEU A 577 " pdb=" CB LEU A 577 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.27e-01 ... (remaining 3981 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 28 " 0.073 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO E 29 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO E 29 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO E 29 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 455 " -0.064 5.00e-02 4.00e+02 9.63e-02 1.49e+01 pdb=" N PRO F 456 " 0.167 5.00e-02 4.00e+02 pdb=" CA PRO F 456 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO F 456 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN E 300 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C ASN E 300 " 0.035 2.00e-02 2.50e+03 pdb=" O ASN E 300 " -0.013 2.00e-02 2.50e+03 pdb=" N GLY E 301 " -0.012 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 190 2.50 - 3.10: 18612 3.10 - 3.70: 38662 3.70 - 4.30: 53365 4.30 - 4.90: 88206 Nonbonded interactions: 199035 Sorted by model distance: nonbonded pdb=" O3A ATP D1001 " pdb="MG MG D1002 " model vdw 1.900 2.170 nonbonded pdb=" O2B ATP C1001 " pdb="MG MG C1002 " model vdw 1.937 2.170 nonbonded pdb=" O3G ATP C1001 " pdb="MG MG C1002 " model vdw 1.971 2.170 nonbonded pdb=" O2B ATP B1001 " pdb="MG MG B1002 " model vdw 1.991 2.170 nonbonded pdb=" O2B ATP A1001 " pdb="MG MG A1002 " model vdw 2.013 2.170 ... (remaining 199030 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 323 through 701) selection = (chain 'B' and resid 323 through 701) selection = (chain 'C' and resid 323 through 701) selection = chain 'F' } ncs_group { reference = (chain 'D' and resid 1 through 700) selection = (chain 'E' and resid 1 through 700) } 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: 1.520 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: 0.020 Extract box with map and model: 8.480 Check model and map are aligned: 0.400 Set scattering table: 0.240 Process input model: 67.820 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.150 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 0.084 26281 Z= 0.197 Angle : 0.633 11.893 35593 Z= 0.358 Chirality : 0.042 0.189 3984 Planarity : 0.004 0.108 4537 Dihedral : 16.504 157.050 10087 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.23 % Rotamer: Outliers : 0.59 % Allowed : 18.73 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.13 (0.15), residues: 3133 helix: 0.54 (0.17), residues: 1040 sheet: -1.30 (0.25), residues: 452 loop : -1.44 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 675 HIS 0.014 0.001 HIS F 629 PHE 0.015 0.001 PHE E 240 TYR 0.019 0.001 TYR F 645 ARG 0.004 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 228 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.7815 (mmm) cc_final: 0.7591 (tpp) REVERT: A 593 ASN cc_start: 0.8654 (m-40) cc_final: 0.8290 (t0) REVERT: A 618 MET cc_start: 0.7102 (ptp) cc_final: 0.6864 (pmm) REVERT: D 1 MET cc_start: 0.3721 (ttt) cc_final: 0.3517 (ttt) REVERT: E 116 MET cc_start: 0.7572 (ptp) cc_final: 0.7011 (ppp) REVERT: E 223 LEU cc_start: 0.8394 (mm) cc_final: 0.8129 (tp) REVERT: E 455 SER cc_start: 0.7647 (OUTLIER) cc_final: 0.7308 (t) outliers start: 17 outliers final: 5 residues processed: 240 average time/residue: 0.3591 time to fit residues: 139.2853 Evaluate side-chains 216 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 210 time to evaluate : 3.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 498 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 0.0770 chunk 125 optimal weight: 7.9990 chunk 243 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 148 optimal weight: 0.6980 chunk 181 optimal weight: 0.5980 chunk 282 optimal weight: 5.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN B 466 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 629 HIS F 641 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26281 Z= 0.174 Angle : 0.523 9.168 35593 Z= 0.270 Chirality : 0.042 0.157 3984 Planarity : 0.004 0.076 4537 Dihedral : 10.139 156.749 3679 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 1.87 % Allowed : 18.24 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3133 helix: 0.46 (0.16), residues: 1054 sheet: -1.21 (0.25), residues: 439 loop : -1.36 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 350 HIS 0.009 0.001 HIS F 548 PHE 0.020 0.001 PHE K 100 TYR 0.017 0.001 TYR E 82 ARG 0.004 0.000 ARG K 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 216 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 ASN cc_start: 0.8696 (m-40) cc_final: 0.8252 (t0) REVERT: A 602 ILE cc_start: 0.9283 (mt) cc_final: 0.9072 (mm) REVERT: A 618 MET cc_start: 0.7316 (ptp) cc_final: 0.6828 (pmm) REVERT: D 62 TYR cc_start: 0.6888 (m-80) cc_final: 0.6652 (m-80) REVERT: D 144 MET cc_start: 0.8633 (tpt) cc_final: 0.8429 (tpt) REVERT: D 150 MET cc_start: 0.7796 (mmm) cc_final: 0.7439 (mmm) REVERT: D 377 LYS cc_start: 0.8874 (tptt) cc_final: 0.8465 (tptm) REVERT: D 684 MET cc_start: 0.8580 (ttp) cc_final: 0.8254 (ttp) REVERT: E 1 MET cc_start: 0.0373 (tpt) cc_final: 0.0079 (tpt) REVERT: E 223 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8168 (tp) REVERT: E 300 ASN cc_start: 0.8419 (t0) cc_final: 0.8144 (t0) REVERT: E 618 MET cc_start: 0.7768 (mtm) cc_final: 0.7334 (mtm) REVERT: K 104 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7889 (mm-30) outliers start: 54 outliers final: 25 residues processed: 258 average time/residue: 0.3301 time to fit residues: 142.3956 Evaluate side-chains 226 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 3.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain K residue 135 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 282 optimal weight: 7.9990 chunk 305 optimal weight: 1.9990 chunk 251 optimal weight: 0.9990 chunk 280 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 226 optimal weight: 0.0040 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 573 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 26281 Z= 0.192 Angle : 0.509 8.139 35593 Z= 0.262 Chirality : 0.041 0.179 3984 Planarity : 0.004 0.067 4537 Dihedral : 9.758 156.413 3673 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.25 % Favored : 95.72 % Rotamer: Outliers : 2.71 % Allowed : 18.28 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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 (0.15), residues: 3133 helix: 0.50 (0.16), residues: 1054 sheet: -1.14 (0.25), residues: 460 loop : -1.28 (0.15), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 350 HIS 0.003 0.001 HIS D 109 PHE 0.015 0.001 PHE K 100 TYR 0.017 0.001 TYR A 482 ARG 0.002 0.000 ARG D 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 214 time to evaluate : 3.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 ASN cc_start: 0.8785 (m-40) cc_final: 0.8273 (t0) REVERT: B 575 LYS cc_start: 0.8666 (mttp) cc_final: 0.8425 (mmtm) REVERT: D 62 TYR cc_start: 0.6972 (m-80) cc_final: 0.6723 (m-80) REVERT: D 110 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8245 (tp30) REVERT: D 150 MET cc_start: 0.8009 (mmm) cc_final: 0.7640 (mmm) REVERT: D 377 LYS cc_start: 0.8829 (tptt) cc_final: 0.8623 (tptp) REVERT: E 223 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8223 (tp) REVERT: E 382 GLU cc_start: 0.8171 (mp0) cc_final: 0.7895 (mp0) REVERT: E 579 GLU cc_start: 0.7960 (mp0) cc_final: 0.7635 (mp0) REVERT: E 618 MET cc_start: 0.7885 (mtm) cc_final: 0.7516 (mtm) REVERT: K 104 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7987 (mm-30) outliers start: 78 outliers final: 50 residues processed: 272 average time/residue: 0.3252 time to fit residues: 148.7474 Evaluate side-chains 250 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 199 time to evaluate : 2.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 259 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 474 GLU Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 661 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 440 VAL Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 135 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 283 optimal weight: 9.9990 chunk 300 optimal weight: 3.9990 chunk 148 optimal weight: 0.0980 chunk 269 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS A 593 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 593 ASN ** E 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 632 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 26281 Z= 0.298 Angle : 0.584 7.265 35593 Z= 0.301 Chirality : 0.043 0.274 3984 Planarity : 0.004 0.065 4537 Dihedral : 9.652 156.203 3673 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.52 % Favored : 94.45 % Rotamer: Outliers : 3.68 % Allowed : 18.59 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -1.11 (0.15), residues: 3133 helix: 0.37 (0.16), residues: 1077 sheet: -1.29 (0.24), residues: 458 loop : -1.32 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 350 HIS 0.005 0.001 HIS D 109 PHE 0.019 0.001 PHE D 626 TYR 0.024 0.001 TYR A 482 ARG 0.004 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 207 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8557 (mmm) cc_final: 0.8319 (mmm) REVERT: A 593 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8229 (t0) REVERT: B 383 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9334 (mp) REVERT: D 110 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8241 (tp30) REVERT: D 150 MET cc_start: 0.8060 (mmm) cc_final: 0.7565 (mmm) REVERT: D 377 LYS cc_start: 0.8946 (tptt) cc_final: 0.8693 (tptp) REVERT: D 462 MET cc_start: 0.8620 (OUTLIER) cc_final: 0.8235 (mmm) REVERT: E 5 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.6762 (mm) REVERT: E 223 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8292 (tp) REVERT: E 618 MET cc_start: 0.8084 (mtm) cc_final: 0.7647 (mtm) outliers start: 106 outliers final: 67 residues processed: 292 average time/residue: 0.3116 time to fit residues: 153.7190 Evaluate side-chains 255 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 183 time to evaluate : 2.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 583 ILE Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain B residue 383 LEU Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 593 ASN Chi-restraints excluded: chain C residue 618 MET Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 194 ILE Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 498 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 274 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 621 ILE Chi-restraints excluded: chain E residue 659 ILE Chi-restraints excluded: chain E residue 661 ASN Chi-restraints excluded: chain E residue 695 ASP Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain K residue 58 ASP Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 0.0010 chunk 170 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 256 optimal weight: 0.0470 chunk 207 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 5.9990 chunk 269 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 overall best weight: 0.9488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN F 347 HIS K 198 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 26281 Z= 0.155 Angle : 0.509 8.272 35593 Z= 0.262 Chirality : 0.041 0.189 3984 Planarity : 0.004 0.064 4537 Dihedral : 9.426 155.834 3673 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.21 % Favored : 95.75 % Rotamer: Outliers : 3.12 % Allowed : 19.74 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.90 (0.15), residues: 3133 helix: 0.55 (0.16), residues: 1070 sheet: -1.18 (0.24), residues: 455 loop : -1.18 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 350 HIS 0.007 0.001 HIS F 548 PHE 0.014 0.001 PHE D 68 TYR 0.015 0.001 TYR A 482 ARG 0.004 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 206 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8525 (mmm) cc_final: 0.8286 (mmm) REVERT: A 593 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8365 (t0) REVERT: A 618 MET cc_start: 0.7191 (pmm) cc_final: 0.6937 (pmm) REVERT: B 532 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8535 (tp) REVERT: D 110 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8261 (tp30) REVERT: D 150 MET cc_start: 0.8002 (mmm) cc_final: 0.7552 (mmm) REVERT: D 462 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8219 (mmm) REVERT: E 116 MET cc_start: 0.7751 (OUTLIER) cc_final: 0.7334 (ppp) REVERT: E 223 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8261 (tp) REVERT: K 1 MET cc_start: 0.2438 (tpp) cc_final: 0.1922 (tpp) outliers start: 90 outliers final: 56 residues processed: 276 average time/residue: 0.3313 time to fit residues: 154.3281 Evaluate side-chains 256 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 195 time to evaluate : 3.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 520 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 632 GLN Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 695 ASP Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 462 MET Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 661 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 396 ILE Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 182 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 176 optimal weight: 0.0020 chunk 74 optimal weight: 0.6980 chunk 300 optimal weight: 0.8980 chunk 249 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 25 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 chunk 157 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 641 ASN ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 632 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 26281 Z= 0.135 Angle : 0.497 8.354 35593 Z= 0.254 Chirality : 0.041 0.176 3984 Planarity : 0.003 0.061 4537 Dihedral : 9.093 156.041 3671 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 2.88 % Allowed : 20.12 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.75 (0.15), residues: 3133 helix: 0.63 (0.16), residues: 1068 sheet: -0.99 (0.25), residues: 451 loop : -1.10 (0.15), residues: 1614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 350 HIS 0.007 0.001 HIS F 548 PHE 0.014 0.001 PHE D 68 TYR 0.014 0.001 TYR K 82 ARG 0.007 0.000 ARG K 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 218 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8529 (mmm) cc_final: 0.8287 (mmm) REVERT: A 618 MET cc_start: 0.7206 (pmm) cc_final: 0.6919 (pmm) REVERT: A 684 MET cc_start: 0.5282 (tpp) cc_final: 0.4992 (tpt) REVERT: B 532 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8633 (tp) REVERT: D 110 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8246 (tp30) REVERT: D 150 MET cc_start: 0.7948 (mmm) cc_final: 0.7623 (mmm) REVERT: E 5 ILE cc_start: 0.7381 (OUTLIER) cc_final: 0.6757 (mm) REVERT: E 116 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7404 (ppp) REVERT: E 223 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8215 (tp) REVERT: E 618 MET cc_start: 0.8020 (mtm) cc_final: 0.7365 (mtp) REVERT: K 1 MET cc_start: 0.2899 (tpp) cc_final: 0.2442 (tpp) outliers start: 83 outliers final: 57 residues processed: 278 average time/residue: 0.3250 time to fit residues: 152.5731 Evaluate side-chains 254 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 193 time to evaluate : 2.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 505 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 116 MET Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 661 ASN Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 548 HIS Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain K residue 116 MET Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 253 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 299 optimal weight: 0.3980 chunk 187 optimal weight: 10.0000 chunk 182 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 597 HIS ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 590 ASN K 195 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26281 Z= 0.178 Angle : 0.513 10.125 35593 Z= 0.260 Chirality : 0.041 0.191 3984 Planarity : 0.003 0.060 4537 Dihedral : 9.033 156.233 3671 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 2.88 % Allowed : 20.57 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 3133 helix: 0.69 (0.16), residues: 1078 sheet: -0.94 (0.24), residues: 483 loop : -1.07 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 350 HIS 0.019 0.001 HIS F 548 PHE 0.014 0.001 PHE D 68 TYR 0.017 0.001 TYR E 699 ARG 0.002 0.000 ARG F 551 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 205 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8596 (mmm) cc_final: 0.8355 (mmm) REVERT: A 618 MET cc_start: 0.7202 (pmm) cc_final: 0.6890 (pmm) REVERT: B 532 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8611 (tp) REVERT: B 614 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7931 (p0) REVERT: D 110 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8251 (tp30) REVERT: D 150 MET cc_start: 0.7776 (mmm) cc_final: 0.7490 (mmm) REVERT: D 377 LYS cc_start: 0.8754 (tptt) cc_final: 0.8533 (tptm) REVERT: E 5 ILE cc_start: 0.7339 (OUTLIER) cc_final: 0.6636 (mm) REVERT: E 116 MET cc_start: 0.8016 (ptp) cc_final: 0.7760 (ppp) REVERT: E 155 LEU cc_start: 0.9339 (tt) cc_final: 0.9063 (pp) REVERT: E 223 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8191 (tp) REVERT: E 618 MET cc_start: 0.8055 (mtm) cc_final: 0.7661 (mtm) REVERT: K 1 MET cc_start: 0.2767 (tpp) cc_final: 0.2293 (tpp) outliers start: 83 outliers final: 64 residues processed: 270 average time/residue: 0.3180 time to fit residues: 145.1284 Evaluate side-chains 260 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 192 time to evaluate : 3.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 538 LYS Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 661 ASN Chi-restraints excluded: chain E residue 669 LEU Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain K residue 116 MET Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 179 THR Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 58 optimal weight: 8.9990 chunk 190 optimal weight: 0.8980 chunk 204 optimal weight: 0.2980 chunk 148 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 272 optimal weight: 8.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN B 463 ASN F 548 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26281 Z= 0.195 Angle : 0.532 10.934 35593 Z= 0.269 Chirality : 0.041 0.180 3984 Planarity : 0.004 0.059 4537 Dihedral : 9.013 156.071 3671 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.50 % Rotamer: Outliers : 3.09 % Allowed : 20.85 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.66 (0.15), residues: 3133 helix: 0.72 (0.16), residues: 1073 sheet: -0.95 (0.24), residues: 483 loop : -1.06 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 350 HIS 0.003 0.001 HIS D 109 PHE 0.022 0.001 PHE E 120 TYR 0.017 0.001 TYR A 482 ARG 0.003 0.000 ARG K 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 199 time to evaluate : 2.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8641 (mmm) cc_final: 0.8403 (mmm) REVERT: A 593 ASN cc_start: 0.8889 (OUTLIER) cc_final: 0.8372 (t0) REVERT: B 532 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8631 (tp) REVERT: B 614 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8307 (p0) REVERT: D 377 LYS cc_start: 0.8777 (tptt) cc_final: 0.8548 (tptm) REVERT: E 1 MET cc_start: -0.0484 (tpt) cc_final: -0.0834 (tpt) REVERT: E 116 MET cc_start: 0.7981 (ptp) cc_final: 0.7754 (ppp) REVERT: E 380 SER cc_start: 0.9372 (OUTLIER) cc_final: 0.9036 (t) REVERT: E 618 MET cc_start: 0.8093 (mtm) cc_final: 0.7667 (mtm) REVERT: F 682 PRO cc_start: 0.7996 (Cg_endo) cc_final: 0.7784 (Cg_exo) REVERT: K 1 MET cc_start: 0.2750 (tpp) cc_final: 0.2272 (tpp) outliers start: 89 outliers final: 70 residues processed: 270 average time/residue: 0.3449 time to fit residues: 156.5204 Evaluate side-chains 262 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 188 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 155 LEU Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 661 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain K residue 116 MET Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 7.9990 chunk 262 optimal weight: 0.3980 chunk 279 optimal weight: 10.0000 chunk 168 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 278 optimal weight: 9.9990 chunk 183 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 593 ASN ** E 546 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26281 Z= 0.200 Angle : 0.538 11.202 35593 Z= 0.271 Chirality : 0.041 0.202 3984 Planarity : 0.004 0.060 4537 Dihedral : 8.994 155.980 3671 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.69 % Favored : 95.28 % Rotamer: Outliers : 2.91 % Allowed : 21.26 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % 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: -0.65 (0.15), residues: 3133 helix: 0.70 (0.16), residues: 1079 sheet: -0.92 (0.24), residues: 483 loop : -1.04 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 350 HIS 0.003 0.001 HIS E 201 PHE 0.019 0.001 PHE E 120 TYR 0.017 0.001 TYR A 482 ARG 0.003 0.000 ARG A 595 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6266 Ramachandran restraints generated. 3133 Oldfield, 0 Emsley, 3133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 186 time to evaluate : 3.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 MET cc_start: 0.8676 (mmm) cc_final: 0.8440 (mmm) REVERT: B 532 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8564 (tp) REVERT: B 614 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8103 (p0) REVERT: D 377 LYS cc_start: 0.8740 (tptt) cc_final: 0.8492 (tptp) REVERT: E 1 MET cc_start: -0.0479 (tpt) cc_final: -0.0763 (tpt) REVERT: E 116 MET cc_start: 0.7970 (ptp) cc_final: 0.7752 (ppp) REVERT: E 155 LEU cc_start: 0.9343 (tt) cc_final: 0.9064 (pp) REVERT: E 380 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.9088 (t) REVERT: E 618 MET cc_start: 0.8117 (mtm) cc_final: 0.7670 (mtm) REVERT: F 682 PRO cc_start: 0.8016 (Cg_endo) cc_final: 0.7803 (Cg_exo) REVERT: K 1 MET cc_start: 0.2808 (tpp) cc_final: 0.2335 (tpp) outliers start: 84 outliers final: 73 residues processed: 254 average time/residue: 0.3158 time to fit residues: 137.3130 Evaluate side-chains 262 residues out of total 2883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 186 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 533 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 373 HIS Chi-restraints excluded: chain B residue 532 LEU Chi-restraints excluded: chain B residue 536 LEU Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 574 ILE Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 659 ILE Chi-restraints excluded: chain B residue 699 TYR Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain C residue 406 THR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 651 LEU Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 23 CYS Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 120 PHE Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 203 ASN Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 260 ASN Chi-restraints excluded: chain D residue 274 LEU Chi-restraints excluded: chain D residue 280 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 432 ASP Chi-restraints excluded: chain D residue 471 LEU Chi-restraints excluded: chain D residue 499 THR Chi-restraints excluded: chain D residue 536 LEU Chi-restraints excluded: chain D residue 632 GLN Chi-restraints excluded: chain D residue 659 ILE Chi-restraints excluded: chain E residue 5 ILE Chi-restraints excluded: chain E residue 19 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 95 ASN Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 223 LEU Chi-restraints excluded: chain E residue 231 VAL Chi-restraints excluded: chain E residue 240 PHE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 290 HIS Chi-restraints excluded: chain E residue 312 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 402 ASP Chi-restraints excluded: chain E residue 462 MET Chi-restraints excluded: chain E residue 485 THR Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 505 THR Chi-restraints excluded: chain E residue 661 ASN Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 402 ASP Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 561 PHE Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 645 TYR Chi-restraints excluded: chain F residue 669 LEU Chi-restraints excluded: chain K residue 32 VAL Chi-restraints excluded: chain K residue 116 MET Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain K residue 182 VAL Chi-restraints excluded: chain K residue 190 ASN Chi-restraints excluded: chain K residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.6929 > 50: distance: 42 - 46: 15.042 distance: 43 - 70: 35.251 distance: 46 - 47: 26.394 distance: 47 - 48: 6.197 distance: 47 - 50: 3.611 distance: 48 - 49: 22.382 distance: 48 - 54: 22.806 distance: 49 - 79: 39.801 distance: 50 - 51: 32.001 distance: 51 - 52: 56.049 distance: 51 - 53: 3.841 distance: 54 - 55: 8.198 distance: 55 - 56: 10.443 distance: 55 - 58: 24.467 distance: 56 - 57: 30.361 distance: 56 - 62: 12.383 distance: 58 - 59: 21.750 distance: 59 - 60: 7.691 distance: 59 - 61: 31.398 distance: 62 - 63: 38.999 distance: 63 - 64: 5.895 distance: 63 - 66: 14.148 distance: 64 - 65: 11.182 distance: 64 - 70: 39.854 distance: 66 - 67: 29.344 distance: 66 - 68: 41.806 distance: 67 - 69: 21.328 distance: 70 - 71: 35.148 distance: 71 - 72: 48.715 distance: 71 - 74: 27.472 distance: 72 - 73: 16.700 distance: 72 - 79: 14.123 distance: 74 - 75: 32.218 distance: 75 - 76: 37.246 distance: 76 - 77: 20.964 distance: 77 - 78: 48.364 distance: 79 - 80: 9.987 distance: 80 - 83: 36.868 distance: 81 - 82: 55.730 distance: 81 - 88: 4.032 distance: 83 - 84: 41.286 distance: 84 - 85: 42.538 distance: 85 - 86: 34.801 distance: 86 - 87: 19.451 distance: 88 - 89: 40.496 distance: 89 - 90: 21.085 distance: 89 - 92: 5.579 distance: 90 - 91: 60.366 distance: 90 - 96: 32.028 distance: 92 - 93: 17.689 distance: 93 - 94: 19.458 distance: 93 - 95: 20.168 distance: 96 - 97: 19.868 distance: 97 - 98: 20.282 distance: 97 - 100: 47.330 distance: 98 - 99: 23.831 distance: 98 - 103: 43.209 distance: 100 - 101: 41.990 distance: 100 - 102: 6.488 distance: 103 - 104: 40.889 distance: 104 - 105: 41.798 distance: 104 - 107: 26.198 distance: 105 - 106: 47.537 distance: 105 - 112: 40.351 distance: 107 - 108: 30.992 distance: 108 - 109: 49.157 distance: 109 - 110: 5.977 distance: 109 - 111: 24.011 distance: 112 - 113: 38.874 distance: 112 - 118: 41.048 distance: 113 - 114: 11.071 distance: 113 - 116: 39.696 distance: 114 - 115: 20.541 distance: 114 - 119: 16.205 distance: 116 - 117: 39.178 distance: 117 - 118: 40.668 distance: 119 - 120: 23.999 distance: 120 - 121: 27.466 distance: 120 - 123: 33.782 distance: 121 - 122: 42.092 distance: 121 - 125: 30.875 distance: 123 - 124: 30.079