Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 01:52:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pek_20327/04_2023/6pek_20327_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pek_20327/04_2023/6pek_20327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pek_20327/04_2023/6pek_20327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pek_20327/04_2023/6pek_20327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pek_20327/04_2023/6pek_20327_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pek_20327/04_2023/6pek_20327_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 8 Type Number sf(0) Gaussians P 10 5.49 5 Mg 4 5.21 5 S 38 5.16 5 Be 4 3.05 5 C 6949 2.51 5 N 1953 2.21 5 O 2136 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 420": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A GLU 449": "OE1" <-> "OE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "C GLU 331": "OE1" <-> "OE2" Residue "C GLU 420": "OE1" <-> "OE2" Residue "C GLU 442": "OE1" <-> "OE2" Residue "C GLU 452": "OE1" <-> "OE2" Residue "D GLU 468": "OE1" <-> "OE2" Residue "E GLU 420": "OE1" <-> "OE2" Residue "E GLU 442": "OE1" <-> "OE2" Residue "E GLU 468": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11106 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 2206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2206 Classifications: {'peptide': 283} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 270} Chain breaks: 1 Chain: "B" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2238 Classifications: {'peptide': 288} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 275} Chain: "C" Number of atoms: 2238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2238 Classifications: {'peptide': 288} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 275} Chain: "D" Number of atoms: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2278 Classifications: {'peptide': 293} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 280} Chain: "E" Number of atoms: 1886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 1886 Classifications: {'peptide': 243} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 232} Chain breaks: 2 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 105 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.24, per 1000 atoms: 0.56 Number of scatterers: 11106 At special positions: 0 Unit cell: (132, 125.664, 83.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 38 16.00 P 10 15.00 Mg 4 11.99 F 12 9.00 O 2136 8.00 N 1953 7.00 C 6949 6.00 Be 4 4.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.80 Conformation dependent library (CDL) restraints added in 1.7 seconds 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2646 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 66 helices and 5 sheets defined 48.2% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 348 through 363 Proline residue: A 361 - end of helix Processing helix chain 'A' and resid 388 through 398 Processing helix chain 'A' and resid 419 through 432 Processing helix chain 'A' and resid 456 through 471 removed outlier: 3.676A pdb=" N ASP A 470 " --> pdb=" O LEU A 466 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 497 No H-bonds generated for 'chain 'A' and resid 494 through 497' Processing helix chain 'A' and resid 511 through 521 Processing helix chain 'A' and resid 531 through 540 Processing helix chain 'A' and resid 546 through 562 removed outlier: 3.829A pdb=" N LEU A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 559 " --> pdb=" O ASP A 555 " (cutoff:3.500A) Proline residue: A 560 - end of helix Processing helix chain 'A' and resid 566 through 571 Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 598 through 609 Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 348 through 363 Proline residue: B 361 - end of helix Processing helix chain 'B' and resid 388 through 399 Processing helix chain 'B' and resid 418 through 432 removed outlier: 4.390A pdb=" N VAL B 423 " --> pdb=" O GLY B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 469 Processing helix chain 'B' and resid 494 through 499 removed outlier: 3.554A pdb=" N ARG B 499 " --> pdb=" O ALA B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 521 Processing helix chain 'B' and resid 531 through 540 Processing helix chain 'B' and resid 546 through 562 Proline residue: B 560 - end of helix Processing helix chain 'B' and resid 566 through 571 Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 598 through 608 Processing helix chain 'C' and resid 325 through 332 Processing helix chain 'C' and resid 348 through 363 Proline residue: C 361 - end of helix Processing helix chain 'C' and resid 388 through 398 Processing helix chain 'C' and resid 408 through 411 No H-bonds generated for 'chain 'C' and resid 408 through 411' Processing helix chain 'C' and resid 418 through 432 Processing helix chain 'C' and resid 456 through 470 removed outlier: 3.808A pdb=" N ASP C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 491 No H-bonds generated for 'chain 'C' and resid 489 through 491' Processing helix chain 'C' and resid 494 through 499 removed outlier: 3.984A pdb=" N ARG C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 494 through 499' Processing helix chain 'C' and resid 511 through 523 removed outlier: 3.742A pdb=" N CYS C 523 " --> pdb=" O LYS C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 540 Processing helix chain 'C' and resid 546 through 562 Proline residue: C 560 - end of helix Processing helix chain 'C' and resid 566 through 571 Processing helix chain 'C' and resid 582 through 590 removed outlier: 4.025A pdb=" N LYS C 590 " --> pdb=" O THR C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 608 Processing helix chain 'D' and resid 322 through 331 removed outlier: 3.805A pdb=" N LEU D 327 " --> pdb=" O ASN D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 363 Proline residue: D 361 - end of helix Processing helix chain 'D' and resid 388 through 399 Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 443 through 446 No H-bonds generated for 'chain 'D' and resid 443 through 446' Processing helix chain 'D' and resid 456 through 469 Processing helix chain 'D' and resid 489 through 491 No H-bonds generated for 'chain 'D' and resid 489 through 491' Processing helix chain 'D' and resid 494 through 499 removed outlier: 3.757A pdb=" N ARG D 499 " --> pdb=" O ALA D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 521 Processing helix chain 'D' and resid 531 through 540 Processing helix chain 'D' and resid 546 through 563 Proline residue: D 560 - end of helix Processing helix chain 'D' and resid 566 through 571 Processing helix chain 'D' and resid 582 through 588 Processing helix chain 'D' and resid 598 through 609 Processing helix chain 'E' and resid 325 through 332 Processing helix chain 'E' and resid 341 through 343 No H-bonds generated for 'chain 'E' and resid 341 through 343' Processing helix chain 'E' and resid 348 through 363 Proline residue: E 361 - end of helix Processing helix chain 'E' and resid 388 through 399 Processing helix chain 'E' and resid 418 through 432 removed outlier: 4.040A pdb=" N VAL E 423 " --> pdb=" O GLY E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 443 through 446 No H-bonds generated for 'chain 'E' and resid 443 through 446' Processing helix chain 'E' and resid 456 through 468 Processing helix chain 'E' and resid 489 through 491 No H-bonds generated for 'chain 'E' and resid 489 through 491' Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'E' and resid 511 through 521 Processing helix chain 'E' and resid 531 through 539 Processing helix chain 'E' and resid 546 through 553 Processing helix chain 'E' and resid 598 through 609 Processing sheet with id= A, first strand: chain 'A' and resid 502 through 506 removed outlier: 4.285A pdb=" N LYS A 502 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 379 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 504 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE A 381 " --> pdb=" O VAL A 504 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL A 482 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N LEU A 380 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY A 484 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N GLY A 382 " --> pdb=" O GLY A 484 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR A 402 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N PHE A 439 " --> pdb=" O THR A 402 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N PHE A 404 " --> pdb=" O PHE A 439 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 502 through 506 removed outlier: 3.888A pdb=" N LYS B 502 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU B 379 " --> pdb=" O LYS B 502 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL B 504 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE B 381 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU B 378 " --> pdb=" O VAL B 480 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL B 482 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N LEU B 380 " --> pdb=" O VAL B 482 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N GLY B 484 " --> pdb=" O LEU B 380 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N GLY B 382 " --> pdb=" O GLY B 484 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER B 436 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N MET B 483 " --> pdb=" O SER B 436 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE B 438 " --> pdb=" O MET B 483 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ALA B 485 " --> pdb=" O ILE B 438 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ILE B 440 " --> pdb=" O ALA B 485 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR B 402 " --> pdb=" O ILE B 437 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE B 439 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N PHE B 404 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ASP B 441 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE B 406 " --> pdb=" O ASP B 441 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 502 through 506 removed outlier: 3.689A pdb=" N LYS C 502 " --> pdb=" O GLY C 377 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU C 378 " --> pdb=" O VAL C 480 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL C 482 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU C 380 " --> pdb=" O VAL C 482 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLY C 484 " --> pdb=" O LEU C 380 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLY C 382 " --> pdb=" O GLY C 484 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR C 486 " --> pdb=" O GLY C 382 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N SER C 436 " --> pdb=" O LEU C 481 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N MET C 483 " --> pdb=" O SER C 436 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE C 438 " --> pdb=" O MET C 483 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N ALA C 485 " --> pdb=" O ILE C 438 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE C 440 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR C 402 " --> pdb=" O ILE C 437 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE C 439 " --> pdb=" O THR C 402 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N PHE C 404 " --> pdb=" O PHE C 439 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ASP C 441 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE C 406 " --> pdb=" O ASP C 441 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 502 through 506 removed outlier: 3.825A pdb=" N PHE D 381 " --> pdb=" O VAL D 504 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N LEU D 378 " --> pdb=" O VAL D 480 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N VAL D 482 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU D 380 " --> pdb=" O VAL D 482 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N GLY D 484 " --> pdb=" O LEU D 380 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLY D 382 " --> pdb=" O GLY D 484 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER D 436 " --> pdb=" O LEU D 481 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N MET D 483 " --> pdb=" O SER D 436 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ILE D 438 " --> pdb=" O MET D 483 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N ALA D 485 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 440 " --> pdb=" O ALA D 485 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N THR D 402 " --> pdb=" O ILE D 437 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N PHE D 439 " --> pdb=" O THR D 402 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N PHE D 404 " --> pdb=" O PHE D 439 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ASP D 441 " --> pdb=" O PHE D 404 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N ILE D 406 " --> pdb=" O ASP D 441 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 484 through 486 removed outlier: 3.840A pdb=" N VAL E 504 " --> pdb=" O LEU E 379 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE E 381 " --> pdb=" O VAL E 504 " (cutoff:3.500A) 394 hydrogen bonds defined for protein. 1176 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: 2.66 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3759 1.34 - 1.46: 2098 1.46 - 1.58: 5316 1.58 - 1.69: 12 1.69 - 1.81: 66 Bond restraints: 11251 Sorted by residual: bond pdb=" C4 ADP D 701 " pdb=" C5 ADP D 701 " ideal model delta sigma weight residual 1.490 1.385 0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C4 ADP A 701 " pdb=" C5 ADP A 701 " ideal model delta sigma weight residual 1.490 1.387 0.103 2.00e-02 2.50e+03 2.63e+01 bond pdb=" C4 ADP B 701 " pdb=" C5 ADP B 701 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C4 ADP C 701 " pdb=" C5 ADP C 701 " ideal model delta sigma weight residual 1.490 1.388 0.102 2.00e-02 2.50e+03 2.61e+01 bond pdb=" C5 ADP D 701 " pdb=" C6 ADP D 701 " ideal model delta sigma weight residual 1.490 1.396 0.094 2.00e-02 2.50e+03 2.19e+01 ... (remaining 11246 not shown) Histogram of bond angle deviations from ideal: 99.82 - 107.08: 332 107.08 - 114.34: 6744 114.34 - 121.59: 5606 121.59 - 128.85: 2489 128.85 - 136.11: 26 Bond angle restraints: 15197 Sorted by residual: angle pdb=" O1B ADP D 701 " pdb=" PB ADP D 701 " pdb=" O3B ADP D 701 " ideal model delta sigma weight residual 119.90 101.52 18.38 3.00e+00 1.11e-01 3.75e+01 angle pdb=" O1B ADP B 701 " pdb=" PB ADP B 701 " pdb=" O3B ADP B 701 " ideal model delta sigma weight residual 119.90 105.20 14.70 3.00e+00 1.11e-01 2.40e+01 angle pdb=" O1B ADP C 701 " pdb=" PB ADP C 701 " pdb=" O3B ADP C 701 " ideal model delta sigma weight residual 119.90 105.37 14.53 3.00e+00 1.11e-01 2.34e+01 angle pdb=" O1B ADP A 701 " pdb=" PB ADP A 701 " pdb=" O3B ADP A 701 " ideal model delta sigma weight residual 119.90 105.39 14.51 3.00e+00 1.11e-01 2.34e+01 angle pdb=" C1' ADP B 701 " pdb=" C2' ADP B 701 " pdb=" C3' ADP B 701 " ideal model delta sigma weight residual 111.00 100.24 10.76 3.00e+00 1.11e-01 1.29e+01 ... (remaining 15192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 6872 35.25 - 70.51: 84 70.51 - 105.76: 10 105.76 - 141.02: 2 141.02 - 176.27: 7 Dihedral angle restraints: 6975 sinusoidal: 2908 harmonic: 4067 Sorted by residual: dihedral pdb=" O2A ADP A 701 " pdb=" O3A ADP A 701 " pdb=" PA ADP A 701 " pdb=" PB ADP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 116.27 -176.27 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP C 701 " pdb=" O5' ADP C 701 " pdb=" PA ADP C 701 " pdb=" O2A ADP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 112.79 -172.79 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP B 701 " pdb=" O5' ADP B 701 " pdb=" PA ADP B 701 " pdb=" O2A ADP B 701 " ideal model delta sinusoidal sigma weight residual 300.00 139.26 160.74 1 2.00e+01 2.50e-03 4.67e+01 ... (remaining 6972 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1485 0.041 - 0.081: 159 0.081 - 0.122: 102 0.122 - 0.163: 5 0.163 - 0.204: 2 Chirality restraints: 1753 Sorted by residual: chirality pdb=" C1' ADP D 701 " pdb=" C2' ADP D 701 " pdb=" N9 ADP D 701 " pdb=" O4' ADP D 701 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' ADP D 701 " pdb=" C2' ADP D 701 " pdb=" C4' ADP D 701 " pdb=" O3' ADP D 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.69 0.18 2.00e-01 2.50e+01 7.93e-01 chirality pdb=" C3' ADP A 701 " pdb=" C2' ADP A 701 " pdb=" C4' ADP A 701 " pdb=" O3' ADP A 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.65 0.14 2.00e-01 2.50e+01 4.79e-01 ... (remaining 1750 not shown) Planarity restraints: 1960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 559 " 0.018 5.00e-02 4.00e+02 2.71e-02 1.17e+00 pdb=" N PRO C 560 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO C 560 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO C 560 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 356 " 0.005 2.00e-02 2.50e+03 9.77e-03 9.55e-01 pdb=" C GLU C 356 " -0.017 2.00e-02 2.50e+03 pdb=" O GLU C 356 " 0.006 2.00e-02 2.50e+03 pdb=" N ILE C 357 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 356 " 0.004 2.00e-02 2.50e+03 8.48e-03 7.20e-01 pdb=" C GLU B 356 " -0.015 2.00e-02 2.50e+03 pdb=" O GLU B 356 " 0.006 2.00e-02 2.50e+03 pdb=" N ILE B 357 " 0.005 2.00e-02 2.50e+03 ... (remaining 1957 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 109 2.51 - 3.11: 9067 3.11 - 3.71: 16937 3.71 - 4.30: 23839 4.30 - 4.90: 38924 Nonbonded interactions: 88876 Sorted by model distance: nonbonded pdb=" OG1 THR D 389 " pdb="MG MG D 703 " model vdw 1.913 2.170 nonbonded pdb=" O2B ADP D 701 " pdb="MG MG D 703 " model vdw 2.041 2.170 nonbonded pdb=" F1 BEF D 702 " pdb="MG MG D 703 " model vdw 2.043 2.120 nonbonded pdb=" O2B ADP A 701 " pdb="MG MG A 703 " model vdw 2.077 2.170 nonbonded pdb=" O2B ADP B 701 " pdb="MG MG B 703 " model vdw 2.112 2.170 ... (remaining 88871 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' selection = (chain 'B' and (resid 323 through 472 or resid 478 through 610 or resid 701 thro \ ugh 703)) selection = (chain 'C' and (resid 323 through 472 or resid 478 through 610 or resid 701 thro \ ugh 703)) selection = (chain 'D' and (resid 323 through 472 or resid 478 through 610 or resid 701 thro \ ugh 703)) } 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: 0.720 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: 4.390 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 30.900 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.005 0.105 11251 Z= 0.307 Angle : 0.731 18.383 15197 Z= 0.299 Chirality : 0.034 0.204 1753 Planarity : 0.002 0.027 1960 Dihedral : 13.789 176.273 4329 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -2.47 (0.21), residues: 1387 helix: -0.96 (0.18), residues: 748 sheet: -1.95 (0.42), residues: 112 loop : -2.45 (0.26), residues: 527 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 444 time to evaluate : 1.465 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.2862 time to fit residues: 168.2184 Evaluate side-chains 256 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 1.414 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 116 optimal weight: 0.0670 chunk 104 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 70 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 108 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.4720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN B 405 ASN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 400 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 11251 Z= 0.187 Angle : 0.655 7.285 15197 Z= 0.293 Chirality : 0.042 0.202 1753 Planarity : 0.004 0.056 1960 Dihedral : 12.981 179.662 1578 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer Outliers : 0.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -1.45 (0.22), residues: 1387 helix: -0.20 (0.19), residues: 760 sheet: -1.42 (0.44), residues: 115 loop : -1.91 (0.27), residues: 512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 1.484 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.2279 time to fit residues: 110.3526 Evaluate side-chains 227 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 104 optimal weight: 4.9990 chunk 85 optimal weight: 0.4980 chunk 34 optimal weight: 0.0670 chunk 125 optimal weight: 0.3980 chunk 135 optimal weight: 4.9990 chunk 111 optimal weight: 0.0040 chunk 124 optimal weight: 0.0870 chunk 42 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 overall best weight: 0.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 HIS E 487 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 11251 Z= 0.154 Angle : 0.616 7.410 15197 Z= 0.274 Chirality : 0.041 0.221 1753 Planarity : 0.004 0.045 1960 Dihedral : 12.531 174.915 1578 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.96 (0.22), residues: 1387 helix: 0.19 (0.19), residues: 760 sheet: -1.12 (0.45), residues: 115 loop : -1.71 (0.26), residues: 512 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 1.466 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 outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2144 time to fit residues: 97.6112 Evaluate side-chains 235 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.333 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 59 optimal weight: 0.0770 chunk 84 optimal weight: 0.0770 chunk 125 optimal weight: 7.9990 chunk 133 optimal weight: 0.0270 chunk 119 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 487 ASN C 326 ASN D 434 GLN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 11251 Z= 0.225 Angle : 0.633 6.612 15197 Z= 0.289 Chirality : 0.042 0.198 1753 Planarity : 0.004 0.048 1960 Dihedral : 12.082 168.138 1578 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.53 (0.23), residues: 1387 helix: 0.48 (0.19), residues: 754 sheet: -0.80 (0.43), residues: 142 loop : -1.42 (0.28), residues: 491 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2303 time to fit residues: 99.4912 Evaluate side-chains 220 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.371 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 75 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 33 optimal weight: 0.3980 chunk 44 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 455 HIS A 571 ASN B 487 ASN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.090 11251 Z= 0.437 Angle : 0.830 7.966 15197 Z= 0.399 Chirality : 0.047 0.179 1753 Planarity : 0.006 0.065 1960 Dihedral : 12.346 174.512 1578 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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 (0.22), residues: 1387 helix: 0.00 (0.19), residues: 739 sheet: -0.82 (0.45), residues: 121 loop : -1.40 (0.27), residues: 527 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2359 time to fit residues: 97.8939 Evaluate side-chains 217 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 120 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 133 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 128 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN C 487 ASN D 347 GLN D 531 GLN ** E 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 487 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 11251 Z= 0.234 Angle : 0.691 7.854 15197 Z= 0.318 Chirality : 0.043 0.244 1753 Planarity : 0.005 0.052 1960 Dihedral : 12.211 177.714 1578 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.58 (0.22), residues: 1387 helix: 0.32 (0.19), residues: 733 sheet: -0.58 (0.46), residues: 115 loop : -1.22 (0.27), residues: 539 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 295 time to evaluate : 1.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.2427 time to fit residues: 104.3213 Evaluate side-chains 226 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 226 time to evaluate : 1.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 133 optimal weight: 8.9990 chunk 83 optimal weight: 0.0000 chunk 81 optimal weight: 10.0000 chunk 61 optimal weight: 0.0270 chunk 82 optimal weight: 0.8980 overall best weight: 0.5042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 11251 Z= 0.176 Angle : 0.680 15.356 15197 Z= 0.308 Chirality : 0.041 0.205 1753 Planarity : 0.004 0.053 1960 Dihedral : 11.968 175.877 1578 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.54 (0.22), residues: 1387 helix: 0.32 (0.19), residues: 747 sheet: -0.52 (0.44), residues: 128 loop : -1.22 (0.27), residues: 512 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 1.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2018 time to fit residues: 87.0293 Evaluate side-chains 231 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 53 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 26 optimal weight: 0.0050 chunk 25 optimal weight: 0.8980 chunk 84 optimal weight: 8.9990 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 104 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 455 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 11251 Z= 0.187 Angle : 0.668 7.254 15197 Z= 0.302 Chirality : 0.041 0.172 1753 Planarity : 0.004 0.054 1960 Dihedral : 11.819 175.866 1578 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.44 (0.22), residues: 1387 helix: 0.42 (0.19), residues: 747 sheet: -0.44 (0.45), residues: 128 loop : -1.22 (0.27), residues: 512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1952 time to fit residues: 84.9430 Evaluate side-chains 230 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 127 optimal weight: 3.9990 chunk 116 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 74 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 97 optimal weight: 0.0030 chunk 38 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.7170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 455 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 11251 Z= 0.182 Angle : 0.660 7.046 15197 Z= 0.298 Chirality : 0.041 0.165 1753 Planarity : 0.004 0.054 1960 Dihedral : 11.716 178.801 1578 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.36 (0.22), residues: 1387 helix: 0.46 (0.19), residues: 745 sheet: -0.37 (0.45), residues: 128 loop : -1.14 (0.27), residues: 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 288 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 288 average time/residue: 0.1971 time to fit residues: 84.8773 Evaluate side-chains 221 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 221 time to evaluate : 1.458 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.8070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 79 optimal weight: 0.5980 chunk 62 optimal weight: 0.4980 chunk 91 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 109 optimal weight: 0.0470 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11251 Z= 0.176 Angle : 0.665 7.259 15197 Z= 0.301 Chirality : 0.041 0.164 1753 Planarity : 0.004 0.054 1960 Dihedral : 11.567 176.879 1578 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.30 (0.22), residues: 1387 helix: 0.46 (0.19), residues: 749 sheet: -0.36 (0.43), residues: 137 loop : -1.04 (0.28), residues: 501 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2774 Ramachandran restraints generated. 1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 291 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.2001 time to fit residues: 86.6053 Evaluate side-chains 220 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 1.417 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 138 random chunks: chunk 33 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 9.9990 chunk 45 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 455 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 455 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.122462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.104561 restraints weight = 26319.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107795 restraints weight = 18791.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.108904 restraints weight = 12334.941| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 11251 Z= 0.182 Angle : 0.675 8.345 15197 Z= 0.305 Chirality : 0.041 0.171 1753 Planarity : 0.004 0.055 1960 Dihedral : 11.471 175.842 1578 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.62 % 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: -0.34 (0.22), residues: 1387 helix: 0.39 (0.19), residues: 757 sheet: -0.33 (0.43), residues: 137 loop : -1.01 (0.28), residues: 493 =============================================================================== Job complete usr+sys time: 2623.62 seconds wall clock time: 48 minutes 2.78 seconds (2882.78 seconds total)