Starting phenix.real_space_refine on Fri Nov 15 11:32:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3c_35149/11_2024/8i3c_35149.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3c_35149/11_2024/8i3c_35149.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3c_35149/11_2024/8i3c_35149.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3c_35149/11_2024/8i3c_35149.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3c_35149/11_2024/8i3c_35149.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3c_35149/11_2024/8i3c_35149.cif" } resolution = 2.85 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= 0.003 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5660 2.51 5 N 1440 2.21 5 O 1506 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 8664 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4297 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 533} Chain breaks: 4 Chain: "B" Number of atoms: 4297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 4297 Classifications: {'peptide': 552} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 533} Chain breaks: 4 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.50, per 1000 atoms: 0.63 Number of scatterers: 8664 At special positions: 0 Unit cell: (80.51, 100.43, 124.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1506 8.00 N 1440 7.00 C 5660 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 1.0 seconds 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 4 sheets defined 59.8% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 Processing helix chain 'A' and resid 137 through 140 removed outlier: 3.621A pdb=" N LYS A 140 " --> pdb=" O GLN A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 137 through 140' Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 183 through 189 removed outlier: 3.891A pdb=" N SER A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 195 removed outlier: 3.534A pdb=" N CYS A 194 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 195 " --> pdb=" O THR A 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 191 through 195' Processing helix chain 'A' and resid 208 through 219 removed outlier: 3.522A pdb=" N LYS A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 250 removed outlier: 3.925A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.575A pdb=" N PHE A 275 " --> pdb=" O PHE A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.601A pdb=" N PHE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.535A pdb=" N ALA A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 4.057A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE A 357 " --> pdb=" O VAL A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 383 through 397 Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.951A pdb=" N HIS A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 404 " --> pdb=" O GLU A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 399 through 404' Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.615A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TRP A 425 " --> pdb=" O CYS A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 455 removed outlier: 3.517A pdb=" N LEU A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.534A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 458 No H-bonds generated for 'chain 'A' and resid 456 through 458' Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 477 through 492 removed outlier: 3.605A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 486 " --> pdb=" O MET A 482 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 503 Processing helix chain 'A' and resid 513 through 541 removed outlier: 3.874A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 561 removed outlier: 3.896A pdb=" N ILE A 550 " --> pdb=" O LYS A 546 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR A 561 " --> pdb=" O ALA A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.829A pdb=" N LYS A 577 " --> pdb=" O VAL A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 4.058A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 605 removed outlier: 3.532A pdb=" N LEU A 601 " --> pdb=" O GLY A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 628 removed outlier: 3.619A pdb=" N GLU A 627 " --> pdb=" O ARG A 623 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 628 " --> pdb=" O PHE A 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 623 through 628' Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'A' and resid 643 through 660 removed outlier: 3.675A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 653 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 137 through 140 removed outlier: 3.621A pdb=" N LYS B 140 " --> pdb=" O GLN B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 137 through 140' Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 183 through 189 removed outlier: 3.892A pdb=" N SER B 187 " --> pdb=" O GLU B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 195 removed outlier: 3.534A pdb=" N CYS B 194 " --> pdb=" O LEU B 191 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU B 195 " --> pdb=" O THR B 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 191 through 195' Processing helix chain 'B' and resid 208 through 219 removed outlier: 3.524A pdb=" N LYS B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG B 214 " --> pdb=" O GLY B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 250 removed outlier: 3.925A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.575A pdb=" N PHE B 275 " --> pdb=" O PHE B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.600A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.537A pdb=" N ALA B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 4.057A pdb=" N CYS B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 357 " --> pdb=" O VAL B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 357' Processing helix chain 'B' and resid 383 through 397 Processing helix chain 'B' and resid 399 through 404 removed outlier: 3.952A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU B 404 " --> pdb=" O GLU B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 399 through 404' Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.615A pdb=" N PHE B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA B 417 " --> pdb=" O GLN B 413 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP B 425 " --> pdb=" O CYS B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 455 removed outlier: 3.517A pdb=" N LEU B 437 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.534A pdb=" N ASN B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 458 No H-bonds generated for 'chain 'B' and resid 456 through 458' Processing helix chain 'B' and resid 462 through 471 Processing helix chain 'B' and resid 477 through 492 removed outlier: 3.605A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 486 " --> pdb=" O MET B 482 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 503 Processing helix chain 'B' and resid 513 through 541 removed outlier: 3.874A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 561 removed outlier: 3.896A pdb=" N ILE B 550 " --> pdb=" O LYS B 546 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 552 " --> pdb=" O SER B 548 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR B 561 " --> pdb=" O ALA B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 578 removed outlier: 3.828A pdb=" N LYS B 577 " --> pdb=" O VAL B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 4.058A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 605 removed outlier: 3.531A pdb=" N LEU B 601 " --> pdb=" O GLY B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 628 removed outlier: 3.619A pdb=" N GLU B 627 " --> pdb=" O ARG B 623 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU B 628 " --> pdb=" O PHE B 624 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 623 through 628' Processing helix chain 'B' and resid 634 through 643 Processing helix chain 'B' and resid 643 through 660 removed outlier: 3.675A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA B 653 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 660 " --> pdb=" O ALA B 656 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 82 through 91 removed outlier: 6.260A pdb=" N ILE A 83 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ARG A 48 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER A 85 " --> pdb=" O CYS A 46 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS A 46 " --> pdb=" O SER A 85 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL A 87 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N PHE A 42 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU A 128 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ASP A 44 " --> pdb=" O LYS A 126 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS A 126 " --> pdb=" O ASP A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.360A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 277 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 290 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 82 through 91 removed outlier: 6.260A pdb=" N ILE B 83 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ARG B 48 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N SER B 85 " --> pdb=" O CYS B 46 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N CYS B 46 " --> pdb=" O SER B 85 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N VAL B 87 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N PHE B 42 " --> pdb=" O LEU B 128 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 128 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ASP B 44 " --> pdb=" O LYS B 126 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS B 126 " --> pdb=" O ASP B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.359A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 277 " --> pdb=" O PHE B 96 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 290 " --> pdb=" O VAL B 278 " (cutoff:3.500A) 373 hydrogen bonds defined for protein. 1089 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: 2.52 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1314 1.29 - 1.42: 2294 1.42 - 1.55: 5136 1.55 - 1.68: 12 1.68 - 1.81: 92 Bond restraints: 8848 Sorted by residual: bond pdb=" C PHE A 441 " pdb=" O PHE A 441 " ideal model delta sigma weight residual 1.236 1.155 0.081 1.28e-02 6.10e+03 4.00e+01 bond pdb=" C PHE B 441 " pdb=" O PHE B 441 " ideal model delta sigma weight residual 1.236 1.155 0.081 1.34e-02 5.57e+03 3.64e+01 bond pdb=" C ILE A 445 " pdb=" O ILE A 445 " ideal model delta sigma weight residual 1.236 1.175 0.061 1.23e-02 6.61e+03 2.48e+01 bond pdb=" C ILE B 445 " pdb=" O ILE B 445 " ideal model delta sigma weight residual 1.236 1.176 0.060 1.23e-02 6.61e+03 2.37e+01 bond pdb=" C GLY B 438 " pdb=" O GLY B 438 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.35e-02 5.49e+03 2.18e+01 ... (remaining 8843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 11157 1.77 - 3.55: 660 3.55 - 5.32: 130 5.32 - 7.09: 41 7.09 - 8.87: 12 Bond angle restraints: 12000 Sorted by residual: angle pdb=" N VAL B 641 " pdb=" CA VAL B 641 " pdb=" C VAL B 641 " ideal model delta sigma weight residual 112.96 106.90 6.06 1.00e+00 1.00e+00 3.68e+01 angle pdb=" N VAL A 641 " pdb=" CA VAL A 641 " pdb=" C VAL A 641 " ideal model delta sigma weight residual 112.96 106.93 6.03 1.00e+00 1.00e+00 3.64e+01 angle pdb=" N VAL A 414 " pdb=" CA VAL A 414 " pdb=" C VAL A 414 " ideal model delta sigma weight residual 112.96 107.88 5.08 1.00e+00 1.00e+00 2.58e+01 angle pdb=" N VAL B 414 " pdb=" CA VAL B 414 " pdb=" C VAL B 414 " ideal model delta sigma weight residual 112.96 107.90 5.06 1.00e+00 1.00e+00 2.56e+01 angle pdb=" N ASP B 435 " pdb=" CA ASP B 435 " pdb=" C ASP B 435 " ideal model delta sigma weight residual 113.50 107.59 5.91 1.23e+00 6.61e-01 2.31e+01 ... (remaining 11995 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.53: 4981 23.53 - 47.06: 260 47.06 - 70.59: 45 70.59 - 94.13: 14 94.13 - 117.66: 4 Dihedral angle restraints: 5304 sinusoidal: 2146 harmonic: 3158 Sorted by residual: dihedral pdb=" CA ILE A 660 " pdb=" C ILE A 660 " pdb=" N LYS A 661 " pdb=" CA LYS A 661 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ILE B 660 " pdb=" C ILE B 660 " pdb=" N LYS B 661 " pdb=" CA LYS B 661 " ideal model delta harmonic sigma weight residual -180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA LYS B 285 " pdb=" C LYS B 285 " pdb=" N CYS B 286 " pdb=" CA CYS B 286 " ideal model delta harmonic sigma weight residual 180.00 156.90 23.10 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 5301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1037 0.057 - 0.113: 325 0.113 - 0.170: 54 0.170 - 0.226: 9 0.226 - 0.283: 7 Chirality restraints: 1432 Sorted by residual: chirality pdb=" CB VAL B 566 " pdb=" CA VAL B 566 " pdb=" CG1 VAL B 566 " pdb=" CG2 VAL B 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB VAL A 566 " pdb=" CA VAL A 566 " pdb=" CG1 VAL A 566 " pdb=" CG2 VAL A 566 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CB VAL B 559 " pdb=" CA VAL B 559 " pdb=" CG1 VAL B 559 " pdb=" CG2 VAL B 559 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 1429 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 661 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LYS B 661 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS B 661 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS B 662 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 661 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C LYS A 661 " -0.062 2.00e-02 2.50e+03 pdb=" O LYS A 661 " 0.023 2.00e-02 2.50e+03 pdb=" N HIS A 662 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 350 " -0.049 5.00e-02 4.00e+02 7.50e-02 8.99e+00 pdb=" N PRO B 351 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO B 351 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 351 " -0.042 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2793 2.83 - 3.35: 7222 3.35 - 3.87: 13519 3.87 - 4.38: 16632 4.38 - 4.90: 29168 Nonbonded interactions: 69334 Sorted by model distance: nonbonded pdb=" O SER A 472 " pdb=" OG SER A 472 " model vdw 2.313 3.040 nonbonded pdb=" NH2 ARG A 470 " pdb=" O LYS A 661 " model vdw 2.314 3.120 nonbonded pdb=" O SER B 472 " pdb=" OG SER B 472 " model vdw 2.314 3.040 nonbonded pdb=" NH2 ARG B 470 " pdb=" O LYS B 661 " model vdw 2.314 3.120 nonbonded pdb=" OE1 GLU A 462 " pdb=" OH TYR A 480 " model vdw 2.320 3.040 ... (remaining 69329 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.270 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.009 0.081 8848 Z= 0.598 Angle : 1.023 8.868 12000 Z= 0.581 Chirality : 0.058 0.283 1432 Planarity : 0.008 0.075 1460 Dihedral : 15.628 117.658 3276 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.81 % Allowed : 6.50 % Favored : 91.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.17 (0.16), residues: 1084 helix: -4.71 (0.07), residues: 600 sheet: -1.01 (0.57), residues: 80 loop : -3.41 (0.24), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 425 HIS 0.006 0.001 HIS A 427 PHE 0.020 0.002 PHE A 499 TYR 0.035 0.003 TYR A 475 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 157 time to evaluate : 0.938 Fit side-chains REVERT: A 491 MET cc_start: 0.8585 (mmp) cc_final: 0.8367 (mmt) REVERT: B 491 MET cc_start: 0.8600 (mmp) cc_final: 0.8392 (mmp) outliers start: 17 outliers final: 4 residues processed: 167 average time/residue: 1.4878 time to fit residues: 262.8513 Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 120 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 568 LYS Chi-restraints excluded: chain B residue 566 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 531 GLN B 531 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8848 Z= 0.192 Angle : 0.606 6.636 12000 Z= 0.310 Chirality : 0.041 0.161 1432 Planarity : 0.006 0.054 1460 Dihedral : 9.755 99.795 1346 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.84 % Allowed : 12.47 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.85 (0.20), residues: 1084 helix: -2.41 (0.16), residues: 602 sheet: -0.99 (0.52), residues: 80 loop : -2.89 (0.26), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 447 HIS 0.003 0.001 HIS B 434 PHE 0.008 0.001 PHE A 499 TYR 0.027 0.001 TYR A 475 ARG 0.007 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 134 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: A 41 LYS cc_start: 0.7350 (ptpp) cc_final: 0.7009 (mttt) REVERT: A 232 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: A 300 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: A 450 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8320 (tp) REVERT: B 450 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8278 (tp) REVERT: B 626 GLU cc_start: 0.6738 (pt0) cc_final: 0.6255 (pm20) outliers start: 36 outliers final: 8 residues processed: 154 average time/residue: 1.1769 time to fit residues: 194.0134 Evaluate side-chains 136 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.0010 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN A 461 GLN B 461 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8848 Z= 0.218 Angle : 0.594 7.950 12000 Z= 0.295 Chirality : 0.041 0.144 1432 Planarity : 0.005 0.044 1460 Dihedral : 7.252 62.785 1339 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.84 % Allowed : 13.75 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.23), residues: 1084 helix: -1.07 (0.20), residues: 634 sheet: -1.37 (0.47), residues: 90 loop : -2.78 (0.28), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 447 HIS 0.002 0.001 HIS A 434 PHE 0.009 0.001 PHE B 203 TYR 0.026 0.002 TYR B 475 ARG 0.011 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.911 Fit side-chains REVERT: A 41 LYS cc_start: 0.7343 (ptpp) cc_final: 0.7019 (mttt) REVERT: A 141 ARG cc_start: 0.6956 (OUTLIER) cc_final: 0.6132 (mtp85) REVERT: A 232 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: A 450 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8295 (tp) REVERT: A 626 GLU cc_start: 0.6631 (pt0) cc_final: 0.6198 (pm20) REVERT: B 41 LYS cc_start: 0.7328 (ptpp) cc_final: 0.7002 (mttt) REVERT: B 232 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: B 266 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: B 450 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8317 (tp) REVERT: B 626 GLU cc_start: 0.6741 (pt0) cc_final: 0.6309 (pm20) outliers start: 36 outliers final: 13 residues processed: 147 average time/residue: 1.2491 time to fit residues: 195.7471 Evaluate side-chains 140 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 571 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 28 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS A 266 GLN A 662 HIS B 154 HIS B 461 GLN B 662 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 8848 Z= 0.497 Angle : 0.713 6.991 12000 Z= 0.357 Chirality : 0.049 0.154 1432 Planarity : 0.006 0.051 1460 Dihedral : 6.620 66.392 1338 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 5.01 % Allowed : 14.18 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.24), residues: 1084 helix: -1.04 (0.20), residues: 638 sheet: -0.85 (0.53), residues: 80 loop : -2.66 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 447 HIS 0.004 0.001 HIS B 484 PHE 0.012 0.002 PHE B 499 TYR 0.032 0.003 TYR B 475 ARG 0.008 0.001 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.953 Fit side-chains REVERT: A 141 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6148 (mtp85) REVERT: A 232 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8087 (mt-10) REVERT: A 450 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8275 (tp) REVERT: A 626 GLU cc_start: 0.6778 (pt0) cc_final: 0.6317 (pm20) REVERT: B 141 ARG cc_start: 0.7020 (OUTLIER) cc_final: 0.5900 (mtp85) REVERT: B 232 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: B 266 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.7977 (mt0) REVERT: B 450 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8268 (tp) REVERT: B 626 GLU cc_start: 0.6883 (pt0) cc_final: 0.6424 (pm20) outliers start: 47 outliers final: 19 residues processed: 147 average time/residue: 1.2538 time to fit residues: 196.4495 Evaluate side-chains 139 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8848 Z= 0.177 Angle : 0.549 5.620 12000 Z= 0.278 Chirality : 0.041 0.147 1432 Planarity : 0.004 0.040 1460 Dihedral : 6.081 59.663 1338 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.84 % Allowed : 15.78 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.25), residues: 1084 helix: -0.28 (0.21), residues: 622 sheet: -1.09 (0.48), residues: 90 loop : -2.29 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS B 434 PHE 0.011 0.001 PHE B 499 TYR 0.026 0.001 TYR A 475 ARG 0.010 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 125 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 141 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6150 (mtp85) REVERT: A 232 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7993 (mt-10) REVERT: A 266 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7880 (mt0) REVERT: A 450 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8293 (tp) REVERT: A 626 GLU cc_start: 0.6584 (pt0) cc_final: 0.6267 (pm20) REVERT: B 141 ARG cc_start: 0.6975 (OUTLIER) cc_final: 0.5929 (mtp85) REVERT: B 232 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7964 (mt-10) REVERT: B 266 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: B 450 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8294 (tp) REVERT: B 626 GLU cc_start: 0.6680 (pt0) cc_final: 0.6275 (pm20) outliers start: 36 outliers final: 12 residues processed: 147 average time/residue: 1.1447 time to fit residues: 180.4501 Evaluate side-chains 139 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 450 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 102 optimal weight: 0.0570 overall best weight: 1.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8848 Z= 0.345 Angle : 0.624 6.327 12000 Z= 0.312 Chirality : 0.044 0.148 1432 Planarity : 0.005 0.046 1460 Dihedral : 6.034 60.116 1338 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.26 % Allowed : 17.16 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.25), residues: 1084 helix: -0.42 (0.21), residues: 644 sheet: -0.66 (0.54), residues: 80 loop : -2.22 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 447 HIS 0.003 0.001 HIS B 484 PHE 0.013 0.001 PHE B 499 TYR 0.029 0.002 TYR A 475 ARG 0.010 0.001 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 116 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 85 SER cc_start: 0.7914 (p) cc_final: 0.7539 (t) REVERT: A 141 ARG cc_start: 0.7001 (OUTLIER) cc_final: 0.6189 (mtp85) REVERT: A 232 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8066 (mt-10) REVERT: A 266 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7903 (mt0) REVERT: A 450 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8285 (tp) REVERT: A 626 GLU cc_start: 0.6631 (pt0) cc_final: 0.6297 (pm20) REVERT: B 141 ARG cc_start: 0.7005 (OUTLIER) cc_final: 0.5896 (mtp85) REVERT: B 179 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8512 (tp) REVERT: B 232 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: B 266 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7930 (mt0) REVERT: B 450 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8288 (tp) REVERT: B 626 GLU cc_start: 0.6697 (pt0) cc_final: 0.6303 (pm20) outliers start: 40 outliers final: 21 residues processed: 141 average time/residue: 1.2040 time to fit residues: 181.8001 Evaluate side-chains 144 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 141 ARG Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 266 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 565 TYR Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 629 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 65 optimal weight: 0.0060 chunk 42 optimal weight: 0.6980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8848 Z= 0.159 Angle : 0.536 5.719 12000 Z= 0.270 Chirality : 0.040 0.128 1432 Planarity : 0.004 0.052 1460 Dihedral : 5.705 54.442 1338 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.30 % Allowed : 17.70 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.26), residues: 1084 helix: 0.30 (0.22), residues: 612 sheet: -0.82 (0.49), residues: 90 loop : -2.10 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS B 434 PHE 0.011 0.001 PHE B 499 TYR 0.024 0.001 TYR A 475 ARG 0.011 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 85 SER cc_start: 0.7857 (p) cc_final: 0.7416 (t) REVERT: A 136 LYS cc_start: 0.7999 (mptt) cc_final: 0.7768 (tppt) REVERT: A 232 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: A 450 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8292 (tp) REVERT: B 141 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.5994 (mtp85) REVERT: B 193 LYS cc_start: 0.8757 (mtmm) cc_final: 0.8544 (pttm) REVERT: B 232 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: B 266 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: B 450 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8298 (tp) REVERT: B 626 GLU cc_start: 0.6580 (pt0) cc_final: 0.6325 (pm20) outliers start: 31 outliers final: 15 residues processed: 145 average time/residue: 1.0791 time to fit residues: 168.4886 Evaluate side-chains 143 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 581 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 83 optimal weight: 0.1980 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8848 Z= 0.285 Angle : 0.593 5.891 12000 Z= 0.296 Chirality : 0.043 0.141 1432 Planarity : 0.005 0.039 1460 Dihedral : 5.772 56.380 1338 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.41 % Allowed : 18.34 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.26), residues: 1084 helix: 0.07 (0.21), residues: 632 sheet: -0.68 (0.49), residues: 90 loop : -2.13 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 447 HIS 0.002 0.001 HIS B 484 PHE 0.012 0.001 PHE B 499 TYR 0.026 0.002 TYR A 475 ARG 0.007 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.981 Fit side-chains REVERT: A 85 SER cc_start: 0.7793 (p) cc_final: 0.7421 (t) REVERT: A 136 LYS cc_start: 0.8011 (mptt) cc_final: 0.7777 (tppt) REVERT: A 193 LYS cc_start: 0.8759 (mtmm) cc_final: 0.8533 (pttm) REVERT: A 232 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: A 450 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8309 (tp) REVERT: B 136 LYS cc_start: 0.8023 (mptt) cc_final: 0.7796 (tppt) REVERT: B 141 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.5935 (mtp85) REVERT: B 179 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8421 (tp) REVERT: B 193 LYS cc_start: 0.8764 (mtmm) cc_final: 0.8535 (pttm) REVERT: B 232 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: B 266 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: B 450 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8314 (tp) REVERT: B 626 GLU cc_start: 0.6499 (pt0) cc_final: 0.6267 (pm20) outliers start: 32 outliers final: 18 residues processed: 139 average time/residue: 1.1651 time to fit residues: 173.4914 Evaluate side-chains 144 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 581 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8848 Z= 0.209 Angle : 0.556 6.171 12000 Z= 0.278 Chirality : 0.041 0.134 1432 Planarity : 0.005 0.058 1460 Dihedral : 5.644 52.452 1338 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.09 % Allowed : 18.87 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.26), residues: 1084 helix: 0.26 (0.21), residues: 632 sheet: -0.56 (0.49), residues: 90 loop : -2.03 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS B 434 PHE 0.011 0.001 PHE B 499 TYR 0.025 0.002 TYR A 475 ARG 0.013 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.891 Fit side-chains REVERT: A 85 SER cc_start: 0.7856 (p) cc_final: 0.7461 (t) REVERT: A 136 LYS cc_start: 0.7918 (mptt) cc_final: 0.7712 (tppt) REVERT: A 193 LYS cc_start: 0.8734 (mtmm) cc_final: 0.8488 (pttm) REVERT: A 232 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: A 450 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8289 (tp) REVERT: B 141 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.6009 (mtp85) REVERT: B 179 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8369 (tp) REVERT: B 193 LYS cc_start: 0.8742 (mtmm) cc_final: 0.8502 (pttm) REVERT: B 232 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: B 266 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: B 450 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8290 (tp) REVERT: B 626 GLU cc_start: 0.6393 (pt0) cc_final: 0.6144 (pm20) outliers start: 29 outliers final: 16 residues processed: 136 average time/residue: 1.1627 time to fit residues: 169.3194 Evaluate side-chains 142 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.2980 chunk 72 optimal weight: 0.0050 chunk 109 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.0598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8848 Z= 0.211 Angle : 0.556 6.795 12000 Z= 0.277 Chirality : 0.041 0.135 1432 Planarity : 0.004 0.040 1460 Dihedral : 5.628 51.775 1338 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.77 % Allowed : 19.51 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.26), residues: 1084 helix: 0.35 (0.21), residues: 632 sheet: -0.48 (0.50), residues: 90 loop : -1.96 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS B 484 PHE 0.012 0.001 PHE B 499 TYR 0.025 0.002 TYR A 475 ARG 0.008 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2168 Ramachandran restraints generated. 1084 Oldfield, 0 Emsley, 1084 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 85 SER cc_start: 0.7889 (p) cc_final: 0.7515 (t) REVERT: A 179 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8410 (tp) REVERT: A 193 LYS cc_start: 0.8733 (mtmm) cc_final: 0.8492 (pttm) REVERT: A 232 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: A 450 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8292 (tp) REVERT: B 141 ARG cc_start: 0.7029 (OUTLIER) cc_final: 0.6005 (mtp85) REVERT: B 179 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8346 (tp) REVERT: B 193 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8496 (pttm) REVERT: B 232 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: B 266 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: B 450 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8292 (tp) outliers start: 26 outliers final: 15 residues processed: 132 average time/residue: 1.0720 time to fit residues: 152.3845 Evaluate side-chains 138 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 232 GLU Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 252 LEU Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 566 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 141 ARG Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 232 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 266 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 450 LEU Chi-restraints excluded: chain B residue 566 VAL Chi-restraints excluded: chain B residue 581 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.164195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.118748 restraints weight = 9264.621| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.66 r_work: 0.3187 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.2783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8848 Z= 0.237 Angle : 0.567 6.947 12000 Z= 0.283 Chirality : 0.042 0.138 1432 Planarity : 0.004 0.039 1460 Dihedral : 5.642 52.075 1338 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.67 % Allowed : 19.51 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 1084 helix: 0.36 (0.21), residues: 632 sheet: -0.43 (0.50), residues: 90 loop : -1.94 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 447 HIS 0.002 0.001 HIS A 484 PHE 0.012 0.001 PHE B 499 TYR 0.025 0.002 TYR A 475 ARG 0.007 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3478.72 seconds wall clock time: 62 minutes 57.80 seconds (3777.80 seconds total)