Starting phenix.real_space_refine on Fri Mar 15 08:39:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pek_20327/03_2024/6pek_20327_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pek_20327/03_2024/6pek_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_20327/03_2024/6pek_20327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pek_20327/03_2024/6pek_20327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pek_20327/03_2024/6pek_20327_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pek_20327/03_2024/6pek_20327_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.42, per 1000 atoms: 0.58 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: 4.48 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: 1.85 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: 2.83 Time building geometry restraints manager: 4.89 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: 1.000 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: 3.970 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 32.150 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.860 ------------------------------------------------------------------------------- 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 % Allowed : 0.51 % Favored : 99.49 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 607 HIS 0.001 0.000 HIS E 455 PHE 0.004 0.000 PHE D 465 TYR 0.003 0.000 TYR C 604 ARG 0.001 0.000 ARG B 503 *********************** 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 : 1.212 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 REVERT: A 372 ARG cc_start: 0.6130 (ptp90) cc_final: 0.5469 (mmt90) REVERT: A 487 ASN cc_start: 0.7614 (m110) cc_final: 0.6942 (m110) REVERT: B 347 GLN cc_start: 0.8560 (mp10) cc_final: 0.7896 (mp10) REVERT: B 348 ASP cc_start: 0.8438 (p0) cc_final: 0.8116 (p0) REVERT: B 390 MET cc_start: 0.8038 (ttp) cc_final: 0.7834 (ttp) REVERT: B 420 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 516 LEU cc_start: 0.8869 (mt) cc_final: 0.8571 (tp) REVERT: B 593 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8372 (mmtm) REVERT: C 343 ASP cc_start: 0.8227 (p0) cc_final: 0.7513 (p0) REVERT: C 348 ASP cc_start: 0.7627 (p0) cc_final: 0.7290 (p0) REVERT: C 412 THR cc_start: 0.6627 (p) cc_final: 0.6272 (p) REVERT: C 439 PHE cc_start: 0.8184 (t80) cc_final: 0.7492 (t80) REVERT: C 490 GLN cc_start: 0.8527 (mp10) cc_final: 0.8223 (mp10) REVERT: D 420 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8966 (mm-30) REVERT: D 441 ASP cc_start: 0.8770 (t0) cc_final: 0.8506 (t0) REVERT: D 464 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7328 (tm-30) REVERT: D 465 PHE cc_start: 0.8990 (t80) cc_final: 0.8757 (t80) REVERT: D 516 LEU cc_start: 0.8996 (pp) cc_final: 0.8126 (tt) REVERT: D 537 LEU cc_start: 0.8915 (tp) cc_final: 0.7858 (tp) REVERT: D 572 MET cc_start: 0.5426 (ptp) cc_final: 0.5190 (ptt) REVERT: D 585 PHE cc_start: 0.8252 (m-80) cc_final: 0.7864 (m-80) REVERT: D 607 TRP cc_start: 0.8299 (t60) cc_final: 0.8061 (t60) REVERT: E 465 PHE cc_start: 0.8995 (t80) cc_final: 0.8765 (t80) REVERT: E 487 ASN cc_start: 0.6859 (m-40) cc_final: 0.6595 (m-40) REVERT: E 510 ASN cc_start: 0.6437 (m-40) cc_final: 0.6234 (t0) REVERT: E 530 THR cc_start: 0.5623 (p) cc_final: 0.5029 (p) REVERT: E 536 GLN cc_start: 0.6428 (mt0) cc_final: 0.5958 (pp30) REVERT: E 597 SER cc_start: 0.0956 (p) cc_final: 0.0096 (m) REVERT: E 599 GLN cc_start: 0.6695 (tp40) cc_final: 0.6404 (pm20) REVERT: E 600 THR cc_start: 0.6761 (p) cc_final: 0.6257 (p) outliers start: 0 outliers final: 0 residues processed: 444 average time/residue: 0.2845 time to fit residues: 166.5772 Evaluate side-chains 265 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 1.360 ------------------------------------------------------------------------------- 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: 9.9990 chunk 35 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 41 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 80 optimal weight: 5.9990 chunk 125 optimal weight: 0.9990 overall best weight: 2.0126 ------------------------------------------------------------------------------- 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 B 487 ASN C 326 ASN ** D 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 400 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11251 Z= 0.324 Angle : 0.707 7.549 15197 Z= 0.326 Chirality : 0.043 0.230 1753 Planarity : 0.005 0.057 1960 Dihedral : 12.810 179.041 1578 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % 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: -1.55 (0.22), residues: 1387 helix: -0.29 (0.18), residues: 759 sheet: -1.42 (0.43), residues: 123 loop : -1.94 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 607 HIS 0.004 0.002 HIS B 455 PHE 0.020 0.002 PHE A 404 TYR 0.025 0.002 TYR E 604 ARG 0.008 0.001 ARG A 459 *********************** 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 333 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 332 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ARG cc_start: 0.6488 (ptp90) cc_final: 0.5779 (mmt90) REVERT: A 487 ASN cc_start: 0.8356 (m110) cc_final: 0.7516 (m110) REVERT: A 498 ARG cc_start: 0.8012 (mmm-85) cc_final: 0.7771 (mmm-85) REVERT: A 580 ILE cc_start: 0.8847 (pt) cc_final: 0.8610 (mp) REVERT: B 347 GLN cc_start: 0.8682 (mp10) cc_final: 0.8033 (mp10) REVERT: B 348 ASP cc_start: 0.8665 (p0) cc_final: 0.8346 (p0) REVERT: B 420 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7858 (mm-30) REVERT: B 487 ASN cc_start: 0.9159 (m-40) cc_final: 0.8674 (m110) REVERT: B 516 LEU cc_start: 0.9131 (mt) cc_final: 0.8797 (mt) REVERT: B 577 MET cc_start: 0.7810 (tpp) cc_final: 0.7554 (tpt) REVERT: B 590 LYS cc_start: 0.8176 (mttp) cc_final: 0.7248 (tmtt) REVERT: C 343 ASP cc_start: 0.8575 (p0) cc_final: 0.8208 (p0) REVERT: C 348 ASP cc_start: 0.7689 (p0) cc_final: 0.7328 (p0) REVERT: C 390 MET cc_start: 0.8713 (ttp) cc_final: 0.8291 (ttp) REVERT: C 412 THR cc_start: 0.7444 (p) cc_final: 0.7227 (p) REVERT: C 439 PHE cc_start: 0.8269 (t80) cc_final: 0.7605 (t80) REVERT: C 448 CYS cc_start: 0.6466 (t) cc_final: 0.6059 (t) REVERT: D 464 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7605 (tm-30) REVERT: D 466 LEU cc_start: 0.9081 (tp) cc_final: 0.8684 (tp) REVERT: D 468 GLU cc_start: 0.8166 (tp30) cc_final: 0.7843 (tp30) REVERT: D 516 LEU cc_start: 0.9129 (pp) cc_final: 0.8271 (tt) REVERT: D 536 GLN cc_start: 0.7749 (tp40) cc_final: 0.7424 (tm-30) REVERT: D 537 LEU cc_start: 0.9154 (tp) cc_final: 0.8457 (tp) REVERT: D 561 ILE cc_start: 0.8753 (mm) cc_final: 0.8453 (mm) REVERT: D 585 PHE cc_start: 0.8453 (m-80) cc_final: 0.7997 (m-80) REVERT: D 604 TYR cc_start: 0.8438 (m-10) cc_final: 0.8174 (m-10) REVERT: D 606 ARG cc_start: 0.8049 (ttp-110) cc_final: 0.7546 (ttp-110) REVERT: E 347 GLN cc_start: 0.5606 (mp10) cc_final: 0.5405 (mp10) REVERT: E 390 MET cc_start: 0.8049 (tpt) cc_final: 0.7842 (tpt) REVERT: E 434 GLN cc_start: 0.8909 (pp30) cc_final: 0.8708 (pp30) REVERT: E 488 ARG cc_start: 0.8636 (mpt-90) cc_final: 0.8124 (mpp80) REVERT: E 530 THR cc_start: 0.5100 (p) cc_final: 0.4877 (p) REVERT: E 536 GLN cc_start: 0.6239 (mt0) cc_final: 0.5720 (pt0) REVERT: E 599 GLN cc_start: 0.6769 (tp40) cc_final: 0.6302 (pm20) REVERT: E 600 THR cc_start: 0.6627 (p) cc_final: 0.6420 (p) outliers start: 1 outliers final: 0 residues processed: 333 average time/residue: 0.2196 time to fit residues: 102.9730 Evaluate side-chains 230 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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: 0.0370 chunk 38 optimal weight: 0.8980 chunk 104 optimal weight: 0.4980 chunk 85 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 125 optimal weight: 0.2980 chunk 135 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 124 optimal weight: 0.0170 chunk 42 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 overall best weight: 0.2896 ------------------------------------------------------------------------------- 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 347 GLN ** 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: 0.7501 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11251 Z= 0.160 Angle : 0.647 8.310 15197 Z= 0.285 Chirality : 0.041 0.240 1753 Planarity : 0.004 0.043 1960 Dihedral : 12.601 172.909 1578 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: -0.98 (0.22), residues: 1387 helix: 0.08 (0.19), residues: 763 sheet: -0.98 (0.43), residues: 119 loop : -1.58 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 607 HIS 0.002 0.001 HIS A 455 PHE 0.028 0.002 PHE A 341 TYR 0.012 0.001 TYR E 505 ARG 0.005 0.000 ARG E 451 *********************** 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 322 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.380 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: A 372 ARG cc_start: 0.6286 (ptp90) cc_final: 0.5423 (mmt90) REVERT: A 498 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7741 (mmm-85) REVERT: A 580 ILE cc_start: 0.8869 (pt) cc_final: 0.8669 (mp) REVERT: B 347 GLN cc_start: 0.8575 (mp10) cc_final: 0.8051 (mp10) REVERT: B 348 ASP cc_start: 0.8543 (p0) cc_final: 0.8253 (p0) REVERT: B 390 MET cc_start: 0.8097 (ttp) cc_final: 0.7872 (ttp) REVERT: B 420 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7639 (mm-30) REVERT: B 487 ASN cc_start: 0.8936 (m-40) cc_final: 0.8455 (m110) REVERT: B 516 LEU cc_start: 0.9057 (mt) cc_final: 0.8783 (mt) REVERT: B 550 THR cc_start: 0.9020 (p) cc_final: 0.8775 (t) REVERT: C 343 ASP cc_start: 0.8487 (p0) cc_final: 0.8179 (p0) REVERT: C 347 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7191 (pm20) REVERT: C 348 ASP cc_start: 0.7726 (p0) cc_final: 0.7353 (p0) REVERT: C 390 MET cc_start: 0.8568 (ttp) cc_final: 0.8213 (ttp) REVERT: C 412 THR cc_start: 0.7089 (p) cc_final: 0.6798 (p) REVERT: C 439 PHE cc_start: 0.8121 (t80) cc_final: 0.7581 (t80) REVERT: C 448 CYS cc_start: 0.6558 (t) cc_final: 0.6259 (t) REVERT: C 607 TRP cc_start: 0.8535 (t-100) cc_final: 0.8326 (t-100) REVERT: D 390 MET cc_start: 0.8411 (ptt) cc_final: 0.8122 (ptm) REVERT: D 465 PHE cc_start: 0.9267 (t80) cc_final: 0.9040 (t80) REVERT: D 466 LEU cc_start: 0.8987 (tp) cc_final: 0.8593 (tp) REVERT: D 468 GLU cc_start: 0.8047 (tp30) cc_final: 0.7841 (tp30) REVERT: D 516 LEU cc_start: 0.9148 (pp) cc_final: 0.8380 (tt) REVERT: D 561 ILE cc_start: 0.8725 (mm) cc_final: 0.8522 (mm) REVERT: D 585 PHE cc_start: 0.8254 (m-80) cc_final: 0.7950 (m-80) REVERT: E 347 GLN cc_start: 0.5560 (mp10) cc_final: 0.5344 (mp10) REVERT: E 390 MET cc_start: 0.8059 (tpt) cc_final: 0.7763 (tpt) REVERT: E 434 GLN cc_start: 0.8941 (pp30) cc_final: 0.8720 (pp30) REVERT: E 488 ARG cc_start: 0.8584 (mpt-90) cc_final: 0.7935 (mpp80) REVERT: E 530 THR cc_start: 0.4986 (p) cc_final: 0.4782 (p) REVERT: E 536 GLN cc_start: 0.6279 (mt0) cc_final: 0.5867 (pt0) REVERT: E 599 GLN cc_start: 0.6821 (tp40) cc_final: 0.6341 (pm20) REVERT: E 600 THR cc_start: 0.6859 (p) cc_final: 0.6456 (p) REVERT: E 604 TYR cc_start: 0.4463 (m-10) cc_final: 0.4189 (m-10) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2136 time to fit residues: 98.6083 Evaluate side-chains 237 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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: 1.9990 chunk 94 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 59 optimal weight: 0.0870 chunk 84 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 133 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 111 optimal weight: 0.0370 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 434 GLN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11251 Z= 0.186 Angle : 0.625 10.360 15197 Z= 0.278 Chirality : 0.040 0.209 1753 Planarity : 0.004 0.049 1960 Dihedral : 12.204 171.598 1578 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: -0.65 (0.23), residues: 1387 helix: 0.37 (0.19), residues: 752 sheet: -0.76 (0.43), residues: 133 loop : -1.48 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 607 HIS 0.001 0.001 HIS A 455 PHE 0.021 0.002 PHE A 341 TYR 0.016 0.001 TYR D 544 ARG 0.006 0.000 ARG C 499 *********************** 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 310 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ARG cc_start: 0.6375 (ptp90) cc_final: 0.5838 (mmt90) REVERT: A 439 PHE cc_start: 0.8658 (t80) cc_final: 0.8418 (t80) REVERT: A 580 ILE cc_start: 0.8886 (pt) cc_final: 0.8650 (mp) REVERT: A 607 TRP cc_start: 0.8045 (t-100) cc_final: 0.7694 (t-100) REVERT: B 347 GLN cc_start: 0.8587 (mp10) cc_final: 0.8020 (mp10) REVERT: B 348 ASP cc_start: 0.8596 (p0) cc_final: 0.8268 (p0) REVERT: B 390 MET cc_start: 0.8131 (ttp) cc_final: 0.7909 (ttp) REVERT: B 420 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7883 (mm-30) REVERT: B 487 ASN cc_start: 0.9064 (m-40) cc_final: 0.8454 (m110) REVERT: B 544 TYR cc_start: 0.8363 (m-80) cc_final: 0.8042 (m-80) REVERT: B 590 LYS cc_start: 0.8204 (mttp) cc_final: 0.7420 (tmtt) REVERT: C 343 ASP cc_start: 0.8571 (p0) cc_final: 0.8166 (p0) REVERT: C 347 GLN cc_start: 0.7424 (mm-40) cc_final: 0.7194 (pm20) REVERT: C 348 ASP cc_start: 0.7701 (p0) cc_final: 0.7279 (p0) REVERT: C 412 THR cc_start: 0.7278 (p) cc_final: 0.7049 (p) REVERT: C 439 PHE cc_start: 0.7984 (t80) cc_final: 0.7550 (t80) REVERT: C 448 CYS cc_start: 0.6402 (t) cc_final: 0.6015 (t) REVERT: C 572 MET cc_start: 0.7883 (ptp) cc_final: 0.7644 (ptt) REVERT: D 420 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8861 (mm-30) REVERT: D 468 GLU cc_start: 0.8077 (tp30) cc_final: 0.7820 (tp30) REVERT: D 516 LEU cc_start: 0.9144 (pp) cc_final: 0.8384 (tt) REVERT: D 537 LEU cc_start: 0.9040 (tp) cc_final: 0.8736 (tp) REVERT: D 561 ILE cc_start: 0.8766 (mm) cc_final: 0.8555 (mm) REVERT: D 585 PHE cc_start: 0.8193 (m-80) cc_final: 0.7920 (m-80) REVERT: E 390 MET cc_start: 0.8049 (tpt) cc_final: 0.7756 (tpt) REVERT: E 434 GLN cc_start: 0.8927 (pp30) cc_final: 0.8623 (pp30) REVERT: E 487 ASN cc_start: 0.8407 (t0) cc_final: 0.7828 (m-40) REVERT: E 505 TYR cc_start: 0.7535 (t80) cc_final: 0.7197 (t80) REVERT: E 530 THR cc_start: 0.4877 (p) cc_final: 0.4660 (p) REVERT: E 536 GLN cc_start: 0.6400 (mt0) cc_final: 0.5889 (pp30) REVERT: E 599 GLN cc_start: 0.6783 (tp40) cc_final: 0.6307 (pm20) REVERT: E 600 THR cc_start: 0.7090 (p) cc_final: 0.6690 (p) REVERT: E 604 TYR cc_start: 0.4462 (m-10) cc_final: 0.4121 (m-10) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.2247 time to fit residues: 98.4679 Evaluate side-chains 233 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 113 optimal weight: 8.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 33 optimal weight: 0.0470 chunk 44 optimal weight: 0.7980 overall best weight: 1.1482 ------------------------------------------------------------------------------- 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** D 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11251 Z= 0.216 Angle : 0.629 6.597 15197 Z= 0.287 Chirality : 0.041 0.228 1753 Planarity : 0.004 0.047 1960 Dihedral : 12.011 173.317 1578 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: -0.46 (0.23), residues: 1387 helix: 0.48 (0.19), residues: 753 sheet: -0.68 (0.44), residues: 132 loop : -1.30 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 607 HIS 0.002 0.001 HIS A 455 PHE 0.014 0.002 PHE C 341 TYR 0.010 0.001 TYR E 505 ARG 0.006 0.001 ARG C 499 *********************** 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 297 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ARG cc_start: 0.6587 (ptp90) cc_final: 0.5753 (mmt90) REVERT: A 439 PHE cc_start: 0.8707 (t80) cc_final: 0.8422 (t80) REVERT: B 347 GLN cc_start: 0.8659 (mp10) cc_final: 0.8068 (mp10) REVERT: B 348 ASP cc_start: 0.8651 (p0) cc_final: 0.8288 (p0) REVERT: B 354 LEU cc_start: 0.9000 (tp) cc_final: 0.8724 (tp) REVERT: B 390 MET cc_start: 0.8349 (ttp) cc_final: 0.8041 (ttp) REVERT: B 420 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7942 (mm-30) REVERT: B 487 ASN cc_start: 0.9093 (m-40) cc_final: 0.8486 (m110) REVERT: B 590 LYS cc_start: 0.8296 (mttp) cc_final: 0.7464 (tmtt) REVERT: B 602 GLU cc_start: 0.7644 (tp30) cc_final: 0.7189 (tp30) REVERT: C 343 ASP cc_start: 0.8635 (p0) cc_final: 0.8393 (p0) REVERT: C 347 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7295 (pm20) REVERT: C 348 ASP cc_start: 0.7736 (p0) cc_final: 0.7373 (p0) REVERT: C 390 MET cc_start: 0.8534 (ttp) cc_final: 0.8142 (ttp) REVERT: C 439 PHE cc_start: 0.7997 (t80) cc_final: 0.7646 (t80) REVERT: C 448 CYS cc_start: 0.6391 (t) cc_final: 0.6148 (t) REVERT: C 572 MET cc_start: 0.7905 (ptp) cc_final: 0.7700 (ptt) REVERT: D 439 PHE cc_start: 0.8945 (t80) cc_final: 0.8630 (t80) REVERT: D 466 LEU cc_start: 0.9044 (tp) cc_final: 0.8648 (tp) REVERT: D 468 GLU cc_start: 0.8193 (tp30) cc_final: 0.7869 (tp30) REVERT: D 516 LEU cc_start: 0.9167 (pp) cc_final: 0.8388 (tt) REVERT: D 585 PHE cc_start: 0.8207 (m-80) cc_final: 0.7879 (m-80) REVERT: E 390 MET cc_start: 0.8059 (tpt) cc_final: 0.7770 (tpt) REVERT: E 487 ASN cc_start: 0.8419 (t0) cc_final: 0.7399 (m110) REVERT: E 505 TYR cc_start: 0.7576 (t80) cc_final: 0.7338 (t80) REVERT: E 523 CYS cc_start: 0.4192 (p) cc_final: 0.3796 (m) REVERT: E 536 GLN cc_start: 0.6700 (mt0) cc_final: 0.5970 (pp30) REVERT: E 599 GLN cc_start: 0.6774 (tp40) cc_final: 0.6308 (pm20) REVERT: E 600 THR cc_start: 0.7083 (p) cc_final: 0.6692 (p) REVERT: E 604 TYR cc_start: 0.4230 (m-10) cc_final: 0.4016 (m-10) outliers start: 0 outliers final: 0 residues processed: 297 average time/residue: 0.2104 time to fit residues: 92.9099 Evaluate side-chains 230 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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: 3.9990 chunk 26 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 133 optimal weight: 0.0470 chunk 110 optimal weight: 0.0070 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 128 optimal weight: 10.0000 overall best weight: 0.6100 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11251 Z= 0.173 Angle : 0.630 6.781 15197 Z= 0.280 Chirality : 0.041 0.205 1753 Planarity : 0.004 0.048 1960 Dihedral : 11.943 178.342 1578 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -0.32 (0.23), residues: 1387 helix: 0.58 (0.19), residues: 753 sheet: -0.59 (0.44), residues: 132 loop : -1.23 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 607 HIS 0.003 0.001 HIS A 455 PHE 0.019 0.002 PHE C 341 TYR 0.012 0.001 TYR E 505 ARG 0.007 0.000 ARG D 606 *********************** 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 299 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 299 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 372 ARG cc_start: 0.6578 (ptp90) cc_final: 0.5996 (mmt90) REVERT: A 412 THR cc_start: 0.8888 (t) cc_final: 0.8259 (p) REVERT: A 439 PHE cc_start: 0.8708 (t80) cc_final: 0.8424 (t80) REVERT: B 347 GLN cc_start: 0.8603 (mp10) cc_final: 0.8013 (mp10) REVERT: B 348 ASP cc_start: 0.8658 (p0) cc_final: 0.8323 (p0) REVERT: B 390 MET cc_start: 0.8281 (ttp) cc_final: 0.8000 (ttp) REVERT: B 420 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7876 (mm-30) REVERT: B 487 ASN cc_start: 0.9080 (m-40) cc_final: 0.8489 (m110) REVERT: B 558 LEU cc_start: 0.8275 (mt) cc_final: 0.8062 (mp) REVERT: B 602 GLU cc_start: 0.7466 (tp30) cc_final: 0.7090 (tp30) REVERT: C 343 ASP cc_start: 0.8554 (p0) cc_final: 0.8259 (p0) REVERT: C 347 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7277 (pm20) REVERT: C 348 ASP cc_start: 0.7732 (p0) cc_final: 0.7361 (p0) REVERT: C 390 MET cc_start: 0.8572 (ttp) cc_final: 0.8045 (ttp) REVERT: C 439 PHE cc_start: 0.7951 (t80) cc_final: 0.7543 (t80) REVERT: D 441 ASP cc_start: 0.8987 (t70) cc_final: 0.8756 (t0) REVERT: D 466 LEU cc_start: 0.8954 (tp) cc_final: 0.8560 (tp) REVERT: D 468 GLU cc_start: 0.8194 (tp30) cc_final: 0.7795 (tp30) REVERT: D 516 LEU cc_start: 0.9111 (pp) cc_final: 0.8398 (tt) REVERT: D 585 PHE cc_start: 0.8156 (m-80) cc_final: 0.7902 (m-80) REVERT: E 390 MET cc_start: 0.7992 (tpt) cc_final: 0.7712 (tpt) REVERT: E 487 ASN cc_start: 0.8434 (t0) cc_final: 0.7409 (m-40) REVERT: E 488 ARG cc_start: 0.8506 (mpp80) cc_final: 0.8008 (mpp80) REVERT: E 523 CYS cc_start: 0.4151 (p) cc_final: 0.3723 (m) REVERT: E 536 GLN cc_start: 0.6671 (mt0) cc_final: 0.6237 (pp30) REVERT: E 599 GLN cc_start: 0.6893 (tp40) cc_final: 0.6384 (pm20) REVERT: E 600 THR cc_start: 0.7087 (p) cc_final: 0.6662 (p) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.1950 time to fit residues: 85.7032 Evaluate side-chains 239 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 239 time to evaluate : 1.306 ------------------------------------------------------------------------------- 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: 0.9980 chunk 76 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 133 optimal weight: 0.0970 chunk 83 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11251 Z= 0.171 Angle : 0.626 7.362 15197 Z= 0.279 Chirality : 0.040 0.221 1753 Planarity : 0.004 0.046 1960 Dihedral : 11.780 179.179 1578 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % 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: -0.22 (0.23), residues: 1387 helix: 0.68 (0.19), residues: 754 sheet: -0.46 (0.47), residues: 123 loop : -1.23 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 607 HIS 0.001 0.000 HIS A 455 PHE 0.025 0.002 PHE B 341 TYR 0.031 0.001 TYR E 604 ARG 0.009 0.000 ARG C 498 *********************** 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 301 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 PHE cc_start: 0.6630 (m-80) cc_final: 0.6374 (m-10) REVERT: A 372 ARG cc_start: 0.6601 (ptp90) cc_final: 0.5959 (mmt90) REVERT: A 412 THR cc_start: 0.8871 (t) cc_final: 0.8232 (p) REVERT: A 439 PHE cc_start: 0.8673 (t80) cc_final: 0.8422 (t80) REVERT: B 347 GLN cc_start: 0.8543 (mp10) cc_final: 0.7969 (mp10) REVERT: B 348 ASP cc_start: 0.8587 (p0) cc_final: 0.8280 (p0) REVERT: B 390 MET cc_start: 0.8214 (ttp) cc_final: 0.7964 (ttp) REVERT: B 420 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7831 (mm-30) REVERT: B 487 ASN cc_start: 0.9038 (m-40) cc_final: 0.8445 (m110) REVERT: B 558 LEU cc_start: 0.8307 (mt) cc_final: 0.8076 (mp) REVERT: B 602 GLU cc_start: 0.7468 (tp30) cc_final: 0.7076 (tp30) REVERT: C 343 ASP cc_start: 0.8549 (p0) cc_final: 0.8331 (p0) REVERT: C 347 GLN cc_start: 0.7568 (mm-40) cc_final: 0.7263 (pm20) REVERT: C 348 ASP cc_start: 0.7728 (p0) cc_final: 0.7366 (p0) REVERT: C 390 MET cc_start: 0.8473 (ttp) cc_final: 0.8119 (ttp) REVERT: C 439 PHE cc_start: 0.7894 (t80) cc_final: 0.7476 (t80) REVERT: D 358 VAL cc_start: 0.8740 (t) cc_final: 0.8429 (p) REVERT: D 420 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8778 (mm-30) REVERT: D 441 ASP cc_start: 0.8958 (t70) cc_final: 0.8741 (t0) REVERT: D 466 LEU cc_start: 0.8961 (tp) cc_final: 0.8583 (tp) REVERT: D 468 GLU cc_start: 0.8282 (tp30) cc_final: 0.7887 (tp30) REVERT: D 516 LEU cc_start: 0.9123 (pp) cc_final: 0.8439 (tt) REVERT: D 585 PHE cc_start: 0.8190 (m-80) cc_final: 0.7924 (m-80) REVERT: E 390 MET cc_start: 0.8038 (tpt) cc_final: 0.7766 (tpt) REVERT: E 465 PHE cc_start: 0.9100 (t80) cc_final: 0.8899 (t80) REVERT: E 487 ASN cc_start: 0.8678 (t0) cc_final: 0.7492 (m110) REVERT: E 523 CYS cc_start: 0.4340 (p) cc_final: 0.3858 (m) REVERT: E 536 GLN cc_start: 0.6714 (mt0) cc_final: 0.6302 (pp30) REVERT: E 599 GLN cc_start: 0.6922 (tp40) cc_final: 0.6308 (pm20) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 0.2040 time to fit residues: 90.8361 Evaluate side-chains 236 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 1.215 ------------------------------------------------------------------------------- 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: 6.9990 chunk 79 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 84 optimal weight: 0.0010 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 overall best weight: 2.1592 ------------------------------------------------------------------------------- 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** ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11251 Z= 0.330 Angle : 0.750 9.048 15197 Z= 0.349 Chirality : 0.044 0.171 1753 Planarity : 0.005 0.052 1960 Dihedral : 11.915 176.109 1578 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: -0.56 (0.23), residues: 1387 helix: 0.35 (0.19), residues: 754 sheet: -0.76 (0.42), residues: 142 loop : -1.24 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 607 HIS 0.003 0.001 HIS D 455 PHE 0.021 0.002 PHE B 341 TYR 0.011 0.002 TYR E 505 ARG 0.008 0.001 ARG C 498 *********************** 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 298 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 PHE cc_start: 0.6829 (m-80) cc_final: 0.6625 (m-10) REVERT: A 372 ARG cc_start: 0.6964 (ptp90) cc_final: 0.6353 (mmt90) REVERT: A 390 MET cc_start: 0.9180 (mtm) cc_final: 0.8822 (mtp) REVERT: A 537 LEU cc_start: 0.8874 (mt) cc_final: 0.8596 (mt) REVERT: B 348 ASP cc_start: 0.8755 (p0) cc_final: 0.8427 (p0) REVERT: B 390 MET cc_start: 0.8726 (ttp) cc_final: 0.8522 (ttp) REVERT: B 420 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8017 (mm-30) REVERT: B 487 ASN cc_start: 0.9189 (m-40) cc_final: 0.8526 (m110) REVERT: B 558 LEU cc_start: 0.8281 (mt) cc_final: 0.8056 (mp) REVERT: B 601 LEU cc_start: 0.8576 (pp) cc_final: 0.8337 (pp) REVERT: B 602 GLU cc_start: 0.7462 (tp30) cc_final: 0.7024 (tp30) REVERT: C 343 ASP cc_start: 0.8434 (p0) cc_final: 0.8033 (p0) REVERT: C 348 ASP cc_start: 0.7718 (p0) cc_final: 0.7411 (p0) REVERT: C 420 GLU cc_start: 0.8010 (mp0) cc_final: 0.7665 (mp0) REVERT: C 439 PHE cc_start: 0.7947 (t80) cc_final: 0.7561 (t80) REVERT: C 461 LEU cc_start: 0.8811 (mm) cc_final: 0.8291 (mm) REVERT: D 358 VAL cc_start: 0.8926 (t) cc_final: 0.8669 (p) REVERT: D 441 ASP cc_start: 0.9077 (t70) cc_final: 0.8838 (t0) REVERT: D 516 LEU cc_start: 0.9159 (pp) cc_final: 0.8369 (tt) REVERT: D 572 MET cc_start: 0.6458 (tmm) cc_final: 0.6144 (tpp) REVERT: D 585 PHE cc_start: 0.8493 (m-80) cc_final: 0.8052 (m-80) REVERT: E 487 ASN cc_start: 0.8751 (t0) cc_final: 0.8021 (m110) REVERT: E 488 ARG cc_start: 0.8470 (mpp80) cc_final: 0.7472 (mpp80) REVERT: E 523 CYS cc_start: 0.4789 (p) cc_final: 0.3929 (m) REVERT: E 536 GLN cc_start: 0.6734 (mt0) cc_final: 0.6014 (pp30) REVERT: E 599 GLN cc_start: 0.6789 (tp40) cc_final: 0.6405 (pm20) REVERT: E 600 THR cc_start: 0.6714 (p) cc_final: 0.6489 (p) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1837 time to fit residues: 81.8557 Evaluate side-chains 224 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 1.305 ------------------------------------------------------------------------------- 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: 1.9990 chunk 116 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 0.0870 chunk 97 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 chunk 112 optimal weight: 0.9990 chunk 117 optimal weight: 0.0050 chunk 81 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.4130 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5125 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= 0.172 Angle : 0.677 7.679 15197 Z= 0.303 Chirality : 0.041 0.196 1753 Planarity : 0.004 0.051 1960 Dihedral : 11.730 172.321 1578 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.32 (0.23), residues: 1387 helix: 0.49 (0.19), residues: 751 sheet: -0.47 (0.43), residues: 134 loop : -1.10 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 607 HIS 0.003 0.001 HIS A 455 PHE 0.027 0.002 PHE B 381 TYR 0.013 0.001 TYR E 505 ARG 0.005 0.000 ARG C 499 *********************** 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 296 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 PHE cc_start: 0.6711 (m-80) cc_final: 0.6487 (m-10) REVERT: A 372 ARG cc_start: 0.6769 (ptp90) cc_final: 0.6026 (mmt90) REVERT: A 412 THR cc_start: 0.8738 (t) cc_final: 0.8090 (p) REVERT: B 347 GLN cc_start: 0.8205 (mp10) cc_final: 0.7774 (mp10) REVERT: B 348 ASP cc_start: 0.8545 (p0) cc_final: 0.8253 (p0) REVERT: B 420 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7713 (mm-30) REVERT: B 487 ASN cc_start: 0.9010 (m-40) cc_final: 0.8487 (m110) REVERT: B 558 LEU cc_start: 0.8236 (mt) cc_final: 0.7987 (mp) REVERT: B 572 MET cc_start: 0.6751 (tpt) cc_final: 0.6161 (tpt) REVERT: C 348 ASP cc_start: 0.7726 (p0) cc_final: 0.7456 (p0) REVERT: C 420 GLU cc_start: 0.8030 (mp0) cc_final: 0.7652 (mp0) REVERT: C 439 PHE cc_start: 0.7957 (t80) cc_final: 0.7539 (t80) REVERT: C 442 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7555 (mm-30) REVERT: C 461 LEU cc_start: 0.8800 (mm) cc_final: 0.8394 (mm) REVERT: C 499 ARG cc_start: 0.8567 (mmt-90) cc_final: 0.7863 (mmt-90) REVERT: D 358 VAL cc_start: 0.8841 (t) cc_final: 0.8538 (p) REVERT: D 420 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8851 (mm-30) REVERT: D 465 PHE cc_start: 0.9307 (t80) cc_final: 0.9018 (t80) REVERT: D 516 LEU cc_start: 0.9071 (pp) cc_final: 0.8330 (tt) REVERT: D 561 ILE cc_start: 0.8798 (mm) cc_final: 0.8517 (mm) REVERT: D 585 PHE cc_start: 0.8250 (m-80) cc_final: 0.7891 (m-80) REVERT: E 536 GLN cc_start: 0.6789 (mt0) cc_final: 0.6424 (pp30) REVERT: E 599 GLN cc_start: 0.6861 (tp40) cc_final: 0.6422 (pm20) REVERT: E 600 THR cc_start: 0.6820 (p) cc_final: 0.6581 (p) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.2120 time to fit residues: 91.2731 Evaluate side-chains 232 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 232 time to evaluate : 1.390 ------------------------------------------------------------------------------- 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: 0.8980 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 109 optimal weight: 0.0060 chunk 11 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 355 GLN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11251 Z= 0.189 Angle : 0.667 6.946 15197 Z= 0.299 Chirality : 0.041 0.177 1753 Planarity : 0.004 0.052 1960 Dihedral : 11.590 174.147 1578 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: -0.26 (0.23), residues: 1387 helix: 0.53 (0.19), residues: 751 sheet: -0.43 (0.43), residues: 134 loop : -1.06 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 607 HIS 0.002 0.001 HIS A 455 PHE 0.015 0.002 PHE E 465 TYR 0.012 0.001 TYR G 8 ARG 0.005 0.000 ARG C 499 ********************** 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 294 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 368 PHE cc_start: 0.6655 (m-80) cc_final: 0.6389 (m-10) REVERT: A 372 ARG cc_start: 0.6729 (ptp90) cc_final: 0.6155 (mmt90) REVERT: A 390 MET cc_start: 0.9113 (mtm) cc_final: 0.8801 (mtp) REVERT: B 347 GLN cc_start: 0.8221 (mp10) cc_final: 0.7784 (mp10) REVERT: B 348 ASP cc_start: 0.8556 (p0) cc_final: 0.8277 (p0) REVERT: B 420 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7876 (mm-30) REVERT: B 467 ILE cc_start: 0.9497 (tt) cc_final: 0.9249 (tt) REVERT: B 487 ASN cc_start: 0.8999 (m-40) cc_final: 0.8491 (m110) REVERT: B 558 LEU cc_start: 0.8261 (mt) cc_final: 0.8046 (mp) REVERT: B 572 MET cc_start: 0.6795 (tpt) cc_final: 0.6242 (tpt) REVERT: C 348 ASP cc_start: 0.7740 (p0) cc_final: 0.7455 (p0) REVERT: C 420 GLU cc_start: 0.8018 (mp0) cc_final: 0.7616 (mp0) REVERT: C 439 PHE cc_start: 0.7949 (t80) cc_final: 0.7518 (t80) REVERT: C 461 LEU cc_start: 0.8823 (mm) cc_final: 0.8482 (mm) REVERT: D 358 VAL cc_start: 0.8808 (t) cc_final: 0.8472 (p) REVERT: D 390 MET cc_start: 0.8641 (ptt) cc_final: 0.8338 (ptm) REVERT: D 420 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8749 (mm-30) REVERT: D 441 ASP cc_start: 0.8947 (t70) cc_final: 0.8701 (t0) REVERT: D 516 LEU cc_start: 0.9103 (pp) cc_final: 0.8356 (tt) REVERT: D 561 ILE cc_start: 0.8782 (mm) cc_final: 0.8540 (mm) REVERT: D 585 PHE cc_start: 0.8314 (m-80) cc_final: 0.7937 (m-80) REVERT: E 390 MET cc_start: 0.7996 (tpt) cc_final: 0.7748 (tpt) REVERT: E 536 GLN cc_start: 0.6716 (mt0) cc_final: 0.6278 (pp30) REVERT: E 599 GLN cc_start: 0.6826 (tp40) cc_final: 0.6394 (pm20) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.1842 time to fit residues: 80.7749 Evaluate side-chains 233 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 1.301 ------------------------------------------------------------------------------- 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: 3.9990 chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 487 ASN ** D 520 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.118040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099894 restraints weight = 26084.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.102223 restraints weight = 16880.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.103850 restraints weight = 12256.463| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11251 Z= 0.223 Angle : 0.673 6.842 15197 Z= 0.306 Chirality : 0.041 0.167 1753 Planarity : 0.004 0.052 1960 Dihedral : 11.523 172.432 1578 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.32 (0.23), residues: 1387 helix: 0.43 (0.19), residues: 753 sheet: -0.47 (0.43), residues: 134 loop : -0.99 (0.28), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 607 HIS 0.001 0.001 HIS A 455 PHE 0.031 0.002 PHE B 381 TYR 0.013 0.001 TYR G 8 ARG 0.011 0.000 ARG D 606 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2605.94 seconds wall clock time: 47 minutes 27.12 seconds (2847.12 seconds total)