Starting phenix.real_space_refine on Mon Apr 8 05:09:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/04_2024/8u1l_41816_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/04_2024/8u1l_41816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/04_2024/8u1l_41816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/04_2024/8u1l_41816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/04_2024/8u1l_41816_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u1l_41816/04_2024/8u1l_41816_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 7 5.49 5 Mg 2 5.21 5 S 61 5.16 5 C 7959 2.51 5 N 2133 2.21 5 O 2433 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 416": "OE1" <-> "OE2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B GLU 200": "OE1" <-> "OE2" Residue "B GLU 279": "OE1" <-> "OE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B GLU 420": "OE1" <-> "OE2" Residue "B GLU 488": "OE1" <-> "OE2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "C GLU 425": "OE1" <-> "OE2" Residue "C GLU 545": "OE1" <-> "OE2" Residue "C GLU 607": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 12595 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5171 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 14, 'TRANS': 623} Chain breaks: 1 Chain: "B" Number of atoms: 5171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5171 Classifications: {'peptide': 638} Link IDs: {'PTRANS': 14, 'TRANS': 623} Chain breaks: 1 Chain: "C" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1483 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain breaks: 1 Chain: "D" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 706 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.38, per 1000 atoms: 0.51 Number of scatterers: 12595 At special positions: 0 Unit cell: (134.706, 117.546, 100.386, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 61 16.00 P 7 15.00 Mg 2 11.99 O 2433 8.00 N 2133 7.00 C 7959 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.28 Conformation dependent library (CDL) restraints added in 2.3 seconds 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 61 helices and 10 sheets defined 41.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 36 through 60 removed outlier: 3.581A pdb=" N GLU A 42 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 67 removed outlier: 3.630A pdb=" N LEU A 65 " --> pdb=" O PRO A 62 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER A 67 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 132 through 138 Processing helix chain 'A' and resid 187 through 193 removed outlier: 4.186A pdb=" N ALA A 190 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLU A 191 " --> pdb=" O ASP A 188 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 192 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 292 through 294 No H-bonds generated for 'chain 'A' and resid 292 through 294' Processing helix chain 'A' and resid 297 through 308 Processing helix chain 'A' and resid 371 through 373 No H-bonds generated for 'chain 'A' and resid 371 through 373' Processing helix chain 'A' and resid 398 through 420 removed outlier: 3.839A pdb=" N VAL A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 442 removed outlier: 6.394A pdb=" N LYS A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A 435 " --> pdb=" O GLN A 431 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 453 removed outlier: 4.156A pdb=" N THR A 448 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 450 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 451 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 472 Processing helix chain 'A' and resid 490 through 494 Processing helix chain 'A' and resid 499 through 504 Processing helix chain 'A' and resid 515 through 523 removed outlier: 3.665A pdb=" N VAL A 521 " --> pdb=" O GLU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 573 removed outlier: 5.142A pdb=" N GLY A 561 " --> pdb=" O VAL A 557 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU A 562 " --> pdb=" O LYS A 558 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS A 573 " --> pdb=" O ILE A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 607 Processing helix chain 'A' and resid 613 through 619 removed outlier: 4.748A pdb=" N TYR A 618 " --> pdb=" O SER A 614 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N MET A 619 " --> pdb=" O THR A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 643 Processing helix chain 'A' and resid 648 through 664 Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.567A pdb=" N LEU A 685 " --> pdb=" O ARG A 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 30 Processing helix chain 'B' and resid 36 through 59 removed outlier: 3.528A pdb=" N GLU B 42 " --> pdb=" O PHE B 39 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 57 " --> pdb=" O ILE B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 67 removed outlier: 3.872A pdb=" N SER B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 109 through 116 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 187 through 193 removed outlier: 3.629A pdb=" N ALA B 190 " --> pdb=" O GLU B 187 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLU B 191 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 371 through 373 No H-bonds generated for 'chain 'B' and resid 371 through 373' Processing helix chain 'B' and resid 397 through 418 removed outlier: 3.936A pdb=" N ARG B 404 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU B 407 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 408 " --> pdb=" O LYS B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 442 removed outlier: 6.462A pdb=" N LYS B 434 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN B 435 " --> pdb=" O GLN B 431 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 436 " --> pdb=" O PHE B 432 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N HIS B 441 " --> pdb=" O LYS B 437 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 442 " --> pdb=" O LEU B 438 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 453 removed outlier: 3.990A pdb=" N ASP B 452 " --> pdb=" O THR B 448 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU B 453 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 473 Processing helix chain 'B' and resid 490 through 494 Processing helix chain 'B' and resid 499 through 504 Processing helix chain 'B' and resid 515 through 523 removed outlier: 3.512A pdb=" N GLU B 518 " --> pdb=" O PRO B 515 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL B 521 " --> pdb=" O GLU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 558 Processing helix chain 'B' and resid 560 through 570 Processing helix chain 'B' and resid 599 through 607 removed outlier: 3.694A pdb=" N ARG B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 643 Processing helix chain 'B' and resid 648 through 664 Processing helix chain 'B' and resid 672 through 687 Processing helix chain 'C' and resid 429 through 434 Processing helix chain 'C' and resid 442 through 461 Processing helix chain 'C' and resid 478 through 480 No H-bonds generated for 'chain 'C' and resid 478 through 480' Processing helix chain 'C' and resid 514 through 517 No H-bonds generated for 'chain 'C' and resid 514 through 517' Processing helix chain 'C' and resid 527 through 543 Processing helix chain 'C' and resid 554 through 563 Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 579 through 588 Processing helix chain 'C' and resid 599 through 612 removed outlier: 3.542A pdb=" N SER C 612 " --> pdb=" O LEU C 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 47 Processing helix chain 'D' and resid 103 through 111 removed outlier: 3.642A pdb=" N LYS D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS D 108 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU D 109 " --> pdb=" O MET D 105 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 119 No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing sheet with id= A, first strand: chain 'A' and resid 165 through 169 removed outlier: 7.221A pdb=" N HIS A 184 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N VAL A 143 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL A 182 " --> pdb=" O VAL A 143 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N VAL A 145 " --> pdb=" O LYS A 180 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS A 180 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N SER A 147 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLY A 178 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE A 75 " --> pdb=" O PRO A 212 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS A 214 " --> pdb=" O ILE A 75 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N THR A 216 " --> pdb=" O PRO A 77 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP A 278 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL A 217 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 359 through 362 removed outlier: 7.129A pdb=" N LEU A 354 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N GLY A 378 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N TYR A 355 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL A 380 " --> pdb=" O TYR A 355 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 316 " --> pdb=" O VAL A 334 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 531 through 534 removed outlier: 6.152A pdb=" N VAL A 510 " --> pdb=" O ILE A 485 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 576 through 580 Processing sheet with id= E, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.646A pdb=" N VAL B 217 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE B 73 " --> pdb=" O LYS B 214 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 75 " --> pdb=" O THR B 216 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR B 85 " --> pdb=" O ILE B 76 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 178 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER B 147 " --> pdb=" O TYR B 155 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 359 through 362 removed outlier: 6.895A pdb=" N LEU B 354 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY B 378 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N TYR B 355 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL B 380 " --> pdb=" O TYR B 355 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 316 " --> pdb=" O VAL B 334 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 455 through 457 Processing sheet with id= H, first strand: chain 'B' and resid 531 through 534 removed outlier: 6.401A pdb=" N VAL B 510 " --> pdb=" O ILE B 485 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 576 through 579 Processing sheet with id= J, first strand: chain 'C' and resid 426 through 428 removed outlier: 3.649A pdb=" N PHE C 475 " --> pdb=" O LYS C 483 " (cutoff:3.500A) 487 hydrogen bonds defined for protein. 1185 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 5.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4108 1.34 - 1.46: 2486 1.46 - 1.58: 6104 1.58 - 1.70: 10 1.70 - 1.82: 105 Bond restraints: 12813 Sorted by residual: bond pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " ideal model delta sigma weight residual 1.443 1.219 0.224 1.00e-02 1.00e+04 5.02e+02 bond pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 1.443 1.224 0.219 1.00e-02 1.00e+04 4.80e+02 bond pdb=" C4' ATP A 801 " pdb=" O4' ATP A 801 " ideal model delta sigma weight residual 1.444 1.397 0.047 1.10e-02 8.26e+03 1.86e+01 bond pdb=" C3' ATP B 801 " pdb=" O3' ATP B 801 " ideal model delta sigma weight residual 1.423 1.378 0.045 1.10e-02 8.26e+03 1.66e+01 bond pdb=" C3' ATP A 801 " pdb=" O3' ATP A 801 " ideal model delta sigma weight residual 1.423 1.378 0.045 1.10e-02 8.26e+03 1.64e+01 ... (remaining 12808 not shown) Histogram of bond angle deviations from ideal: 80.41 - 95.57: 7 95.57 - 110.74: 3977 110.74 - 125.91: 13107 125.91 - 141.07: 146 141.07 - 156.24: 2 Bond angle restraints: 17239 Sorted by residual: angle pdb=" C5' ATP B 801 " pdb=" O5' ATP B 801 " pdb=" PA ATP B 801 " ideal model delta sigma weight residual 121.27 156.24 -34.97 1.00e+00 1.00e+00 1.22e+03 angle pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " pdb=" PA ATP A 801 " ideal model delta sigma weight residual 121.27 155.38 -34.11 1.00e+00 1.00e+00 1.16e+03 angle pdb=" C3' ATP B 801 " pdb=" C4' ATP B 801 " pdb=" C5' ATP B 801 " ideal model delta sigma weight residual 115.19 83.09 32.10 1.76e+00 3.23e-01 3.33e+02 angle pdb=" C3' ATP A 801 " pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " ideal model delta sigma weight residual 115.19 85.19 30.00 1.76e+00 3.23e-01 2.91e+02 angle pdb=" C4' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O5' ATP A 801 " ideal model delta sigma weight residual 108.83 140.57 -31.74 2.33e+00 1.85e-01 1.86e+02 ... (remaining 17234 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.23: 7120 18.23 - 36.47: 633 36.47 - 54.70: 120 54.70 - 72.93: 30 72.93 - 91.17: 13 Dihedral angle restraints: 7916 sinusoidal: 3380 harmonic: 4536 Sorted by residual: dihedral pdb=" CA MET A 475 " pdb=" C MET A 475 " pdb=" N LYS A 476 " pdb=" CA LYS A 476 " ideal model delta harmonic sigma weight residual 180.00 152.73 27.27 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA MET B 93 " pdb=" C MET B 93 " pdb=" N THR B 94 " pdb=" CA THR B 94 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA LEU C 598 " pdb=" C LEU C 598 " pdb=" N PHE C 599 " pdb=" CA PHE C 599 " ideal model delta harmonic sigma weight residual 180.00 -157.70 -22.30 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 7913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 1816 0.099 - 0.198: 71 0.198 - 0.297: 4 0.297 - 0.396: 1 0.396 - 0.495: 2 Chirality restraints: 1894 Sorted by residual: chirality pdb=" C4' ATP A 801 " pdb=" C3' ATP A 801 " pdb=" C5' ATP A 801 " pdb=" O4' ATP A 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.99 0.50 2.00e-01 2.50e+01 6.13e+00 chirality pdb=" C4' ATP B 801 " pdb=" C3' ATP B 801 " pdb=" C5' ATP B 801 " pdb=" O4' ATP B 801 " both_signs ideal model delta sigma weight residual False -2.49 -2.97 0.47 2.00e-01 2.50e+01 5.63e+00 chirality pdb=" CG LEU C 538 " pdb=" CB LEU C 538 " pdb=" CD1 LEU C 538 " pdb=" CD2 LEU C 538 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 1891 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 542 " 0.089 5.00e-02 4.00e+02 1.28e-01 2.62e+01 pdb=" N PRO A 543 " -0.221 5.00e-02 4.00e+02 pdb=" CA PRO A 543 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO A 543 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 112 " 0.072 5.00e-02 4.00e+02 1.06e-01 1.80e+01 pdb=" N PRO D 113 " -0.183 5.00e-02 4.00e+02 pdb=" CA PRO D 113 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO D 113 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 542 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO B 543 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " -0.032 5.00e-02 4.00e+02 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 175 2.54 - 3.13: 10096 3.13 - 3.72: 20763 3.72 - 4.31: 28505 4.31 - 4.90: 45209 Nonbonded interactions: 104748 Sorted by model distance: nonbonded pdb=" O3G ATP B 801 " pdb="MG MG B 802 " model vdw 1.947 2.170 nonbonded pdb=" O3A ATP A 801 " pdb="MG MG A 802 " model vdw 2.030 2.170 nonbonded pdb=" O1G ATP A 801 " pdb="MG MG A 802 " model vdw 2.099 2.170 nonbonded pdb=" OH TYR A 425 " pdb=" O LEU A 453 " model vdw 2.176 2.440 nonbonded pdb=" OH TYR A 372 " pdb=" OD2 ASP A 443 " model vdw 2.206 2.440 ... (remaining 104743 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' } 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: 0.680 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: 4.160 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 35.390 Find NCS groups from input model: 0.540 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 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 0.224 12813 Z= 0.331 Angle : 1.066 34.971 17239 Z= 0.636 Chirality : 0.046 0.495 1894 Planarity : 0.005 0.128 2194 Dihedral : 14.738 91.169 4980 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.22), residues: 1524 helix: 0.86 (0.21), residues: 643 sheet: 0.85 (0.37), residues: 201 loop : -0.42 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 31 HIS 0.006 0.001 HIS B 314 PHE 0.013 0.001 PHE A 303 TYR 0.009 0.001 TYR B 483 ARG 0.016 0.001 ARG C 518 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.461 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: A 512 MET cc_start: 0.8046 (mmm) cc_final: 0.7781 (mmm) REVERT: B 475 MET cc_start: 0.4892 (mmt) cc_final: 0.4605 (mmt) REVERT: C 457 ASP cc_start: 0.9102 (t70) cc_final: 0.8640 (t0) REVERT: D 105 MET cc_start: 0.3884 (tpp) cc_final: 0.1675 (ptm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2822 time to fit residues: 43.6766 Evaluate side-chains 94 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 61 optimal weight: 20.0000 chunk 119 optimal weight: 40.0000 chunk 46 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 88 optimal weight: 20.0000 chunk 138 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 445 GLN B 492 GLN ** B 523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 436 GLN C 556 GLN D 9 HIS ** D 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 12813 Z= 0.303 Angle : 0.655 8.829 17239 Z= 0.346 Chirality : 0.042 0.289 1894 Planarity : 0.005 0.070 2194 Dihedral : 8.692 79.740 1741 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.81 % Allowed : 12.54 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1524 helix: 0.79 (0.20), residues: 625 sheet: 0.63 (0.39), residues: 199 loop : -0.46 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 423 HIS 0.009 0.002 HIS A 314 PHE 0.016 0.002 PHE A 303 TYR 0.026 0.002 TYR A 595 ARG 0.007 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 88 time to evaluate : 1.563 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: A 38 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8938 (tt) REVERT: B 193 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7743 (mm) REVERT: C 542 MET cc_start: 0.5996 (mmp) cc_final: 0.5737 (mmp) REVERT: D 38 GLU cc_start: 0.8256 (mt-10) cc_final: 0.8053 (mt-10) outliers start: 39 outliers final: 22 residues processed: 119 average time/residue: 0.2514 time to fit residues: 44.2567 Evaluate side-chains 110 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 86 time to evaluate : 1.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 20.0000 chunk 42 optimal weight: 20.0000 chunk 114 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 138 optimal weight: 10.0000 chunk 149 optimal weight: 30.0000 chunk 123 optimal weight: 8.9990 chunk 137 optimal weight: 6.9990 chunk 47 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 HIS B 492 GLN B 523 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12813 Z= 0.207 Angle : 0.568 8.120 17239 Z= 0.301 Chirality : 0.041 0.309 1894 Planarity : 0.004 0.068 2194 Dihedral : 8.489 88.230 1741 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.17 % Allowed : 12.46 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.22), residues: 1524 helix: 0.75 (0.21), residues: 623 sheet: 0.48 (0.38), residues: 207 loop : -0.52 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 423 HIS 0.006 0.001 HIS B 314 PHE 0.021 0.001 PHE D 43 TYR 0.015 0.001 TYR A 372 ARG 0.007 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 87 time to evaluate : 2.108 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: A 31 THR cc_start: 0.8407 (OUTLIER) cc_final: 0.7966 (p) REVERT: A 125 MET cc_start: 0.8261 (mmm) cc_final: 0.7508 (mmp) REVERT: B 622 LYS cc_start: 0.7363 (tptt) cc_final: 0.6828 (tptt) REVERT: C 457 ASP cc_start: 0.8845 (t70) cc_final: 0.8501 (t70) REVERT: C 572 LYS cc_start: 0.8941 (tptp) cc_final: 0.8584 (tttt) REVERT: D 20 HIS cc_start: 0.6626 (OUTLIER) cc_final: 0.6257 (t-90) REVERT: D 105 MET cc_start: 0.1696 (tpt) cc_final: -0.0658 (ptp) outliers start: 44 outliers final: 28 residues processed: 121 average time/residue: 0.2720 time to fit residues: 48.0722 Evaluate side-chains 115 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 85 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 578 VAL Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 477 HIS Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 20 HIS Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 71 optimal weight: 20.0000 chunk 15 optimal weight: 30.0000 chunk 65 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 146 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12813 Z= 0.316 Angle : 0.640 10.708 17239 Z= 0.339 Chirality : 0.042 0.345 1894 Planarity : 0.004 0.073 2194 Dihedral : 8.629 87.066 1741 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 25.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 4.32 % Allowed : 13.33 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.22), residues: 1524 helix: 0.51 (0.21), residues: 624 sheet: 0.28 (0.38), residues: 207 loop : -0.65 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 423 HIS 0.026 0.002 HIS D 20 PHE 0.019 0.002 PHE D 43 TYR 0.020 0.002 TYR A 372 ARG 0.007 0.001 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 85 time to evaluate : 1.435 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: A 123 ILE cc_start: 0.7655 (OUTLIER) cc_final: 0.7168 (mm) REVERT: A 125 MET cc_start: 0.8332 (mmm) cc_final: 0.7523 (mmp) REVERT: A 512 MET cc_start: 0.7883 (mmm) cc_final: 0.7165 (mmm) REVERT: A 601 MET cc_start: 0.6447 (tpp) cc_final: 0.6245 (tpt) REVERT: B 193 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7920 (mm) REVERT: B 441 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.6676 (t-170) REVERT: B 524 MET cc_start: 0.9302 (tpt) cc_final: 0.9097 (tpt) REVERT: B 622 LYS cc_start: 0.7525 (tptt) cc_final: 0.6809 (tptt) REVERT: C 572 LYS cc_start: 0.8966 (tptp) cc_final: 0.8610 (tttt) REVERT: D 14 ASP cc_start: 0.7343 (OUTLIER) cc_final: 0.7094 (p0) REVERT: D 38 GLU cc_start: 0.8306 (mt-10) cc_final: 0.7748 (mp0) outliers start: 60 outliers final: 40 residues processed: 133 average time/residue: 0.2548 time to fit residues: 49.7038 Evaluate side-chains 125 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 81 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 75 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12813 Z= 0.195 Angle : 0.572 9.089 17239 Z= 0.300 Chirality : 0.041 0.334 1894 Planarity : 0.004 0.072 2194 Dihedral : 8.388 87.904 1741 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 20.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.17 % Allowed : 14.70 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.22), residues: 1524 helix: 0.63 (0.21), residues: 624 sheet: 0.37 (0.38), residues: 207 loop : -0.62 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 7 HIS 0.006 0.001 HIS B 314 PHE 0.012 0.001 PHE D 43 TYR 0.015 0.001 TYR A 372 ARG 0.005 0.000 ARG D 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 82 time to evaluate : 1.540 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 123 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7144 (mm) REVERT: A 125 MET cc_start: 0.8048 (mmm) cc_final: 0.7220 (mmp) REVERT: B 125 MET cc_start: 0.8341 (mmm) cc_final: 0.7081 (mmm) REVERT: B 441 HIS cc_start: 0.7381 (OUTLIER) cc_final: 0.6453 (t-170) REVERT: B 524 MET cc_start: 0.9295 (tpt) cc_final: 0.9003 (tpt) REVERT: B 622 LYS cc_start: 0.7602 (tptt) cc_final: 0.7207 (tptt) REVERT: C 457 ASP cc_start: 0.8824 (t70) cc_final: 0.8469 (t70) REVERT: C 572 LYS cc_start: 0.8957 (tptp) cc_final: 0.8564 (tttt) REVERT: D 14 ASP cc_start: 0.7289 (OUTLIER) cc_final: 0.6997 (p0) REVERT: D 38 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7630 (mp0) REVERT: D 39 ARG cc_start: 0.8895 (ttp80) cc_final: 0.8596 (ttp80) REVERT: D 105 MET cc_start: 0.1545 (tpt) cc_final: -0.0291 (ptp) outliers start: 44 outliers final: 29 residues processed: 117 average time/residue: 0.2616 time to fit residues: 45.2939 Evaluate side-chains 112 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 80 time to evaluate : 1.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 122 optimal weight: 0.0970 chunk 68 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 77 optimal weight: 2.9990 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 492 GLN ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12813 Z= 0.238 Angle : 0.586 9.100 17239 Z= 0.308 Chirality : 0.041 0.330 1894 Planarity : 0.004 0.073 2194 Dihedral : 8.390 87.518 1741 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.67 % Allowed : 14.91 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.22), residues: 1524 helix: 0.58 (0.21), residues: 620 sheet: 0.26 (0.38), residues: 208 loop : -0.70 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 7 HIS 0.006 0.001 HIS D 20 PHE 0.012 0.001 PHE D 43 TYR 0.016 0.002 TYR A 372 ARG 0.005 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 82 time to evaluate : 1.601 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: A 123 ILE cc_start: 0.7677 (OUTLIER) cc_final: 0.7140 (mm) REVERT: A 125 MET cc_start: 0.8050 (mmm) cc_final: 0.7382 (mmp) REVERT: A 601 MET cc_start: 0.6549 (tpp) cc_final: 0.6153 (tpp) REVERT: B 37 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8241 (pp20) REVERT: B 193 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8127 (mm) REVERT: B 441 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.6459 (t-170) REVERT: C 457 ASP cc_start: 0.8882 (t70) cc_final: 0.8528 (t70) REVERT: C 572 LYS cc_start: 0.9023 (tptp) cc_final: 0.8746 (tptp) REVERT: D 14 ASP cc_start: 0.7205 (OUTLIER) cc_final: 0.6769 (p0) REVERT: D 38 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8015 (mm-30) REVERT: D 39 ARG cc_start: 0.8970 (ttp80) cc_final: 0.8703 (ttp80) REVERT: D 105 MET cc_start: 0.1750 (tpt) cc_final: 0.0047 (ptp) outliers start: 51 outliers final: 41 residues processed: 123 average time/residue: 0.2816 time to fit residues: 50.1186 Evaluate side-chains 124 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 78 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 14 ASP Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 20.0000 chunk 16 optimal weight: 0.0980 chunk 83 optimal weight: 0.8980 chunk 107 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 146 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 67 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 ASN A 673 GLN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12813 Z= 0.160 Angle : 0.558 10.028 17239 Z= 0.289 Chirality : 0.040 0.276 1894 Planarity : 0.004 0.073 2194 Dihedral : 8.204 88.349 1741 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 18.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.31 % Allowed : 15.63 % Favored : 81.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.22), residues: 1524 helix: 0.71 (0.21), residues: 622 sheet: 0.44 (0.38), residues: 206 loop : -0.61 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 7 HIS 0.005 0.001 HIS B 314 PHE 0.010 0.001 PHE C 559 TYR 0.018 0.001 TYR B 428 ARG 0.004 0.000 ARG D 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 87 time to evaluate : 1.575 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: A 31 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8054 (p) REVERT: A 123 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7167 (mm) REVERT: A 125 MET cc_start: 0.8057 (mmm) cc_final: 0.7201 (mmp) REVERT: B 37 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8196 (pp20) REVERT: B 125 MET cc_start: 0.8424 (mmm) cc_final: 0.7186 (mmt) REVERT: B 193 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8170 (mm) REVERT: B 441 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6523 (t-170) REVERT: C 457 ASP cc_start: 0.8838 (t70) cc_final: 0.8515 (t70) REVERT: C 572 LYS cc_start: 0.8989 (tptp) cc_final: 0.8572 (tttt) REVERT: D 38 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8064 (mm-30) REVERT: D 39 ARG cc_start: 0.8980 (ttp80) cc_final: 0.8746 (ttp80) REVERT: D 105 MET cc_start: 0.1171 (tpt) cc_final: 0.0159 (ptp) outliers start: 46 outliers final: 32 residues processed: 121 average time/residue: 0.2737 time to fit residues: 48.1886 Evaluate side-chains 118 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 81 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 37 GLU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 99 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 133 optimal weight: 20.0000 chunk 140 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12813 Z= 0.288 Angle : 0.651 11.685 17239 Z= 0.338 Chirality : 0.042 0.278 1894 Planarity : 0.004 0.075 2194 Dihedral : 8.427 87.656 1741 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 26.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.67 % Allowed : 16.07 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.22), residues: 1524 helix: 0.52 (0.21), residues: 622 sheet: 0.07 (0.37), residues: 211 loop : -0.73 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 7 HIS 0.008 0.001 HIS C 477 PHE 0.023 0.002 PHE D 124 TYR 0.017 0.002 TYR A 372 ARG 0.006 0.001 ARG C 583 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 83 time to evaluate : 1.581 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: A 123 ILE cc_start: 0.7675 (OUTLIER) cc_final: 0.7239 (mm) REVERT: A 125 MET cc_start: 0.7983 (mmm) cc_final: 0.7324 (mmp) REVERT: A 512 MET cc_start: 0.7939 (mmm) cc_final: 0.7026 (mmm) REVERT: B 125 MET cc_start: 0.8413 (mmm) cc_final: 0.8067 (mmm) REVERT: B 193 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8170 (mm) REVERT: B 441 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.6827 (t-170) REVERT: C 457 ASP cc_start: 0.8975 (t70) cc_final: 0.8615 (t70) REVERT: C 542 MET cc_start: 0.6179 (mmp) cc_final: 0.5414 (mmp) REVERT: C 572 LYS cc_start: 0.9084 (tptp) cc_final: 0.8806 (tptp) REVERT: D 38 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8099 (mt-10) REVERT: D 39 ARG cc_start: 0.9003 (ttp80) cc_final: 0.8801 (ttp80) REVERT: D 105 MET cc_start: 0.1465 (tpt) cc_final: 0.0417 (ptp) outliers start: 51 outliers final: 41 residues processed: 126 average time/residue: 0.2987 time to fit residues: 53.8765 Evaluate side-chains 127 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 83 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 651 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 8.9990 chunk 136 optimal weight: 6.9990 chunk 140 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 123 optimal weight: 20.0000 chunk 129 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 144 optimal weight: 0.5980 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12813 Z= 0.233 Angle : 0.607 10.937 17239 Z= 0.314 Chirality : 0.041 0.266 1894 Planarity : 0.004 0.074 2194 Dihedral : 8.324 87.588 1741 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.53 % Allowed : 16.28 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1524 helix: 0.55 (0.21), residues: 620 sheet: 0.12 (0.38), residues: 201 loop : -0.73 (0.24), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 7 HIS 0.006 0.001 HIS C 477 PHE 0.011 0.001 PHE A 559 TYR 0.016 0.002 TYR A 372 ARG 0.004 0.000 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 87 time to evaluate : 1.517 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: A 512 MET cc_start: 0.7902 (mmm) cc_final: 0.6999 (mmm) REVERT: B 125 MET cc_start: 0.8407 (mmm) cc_final: 0.8009 (mmm) REVERT: B 193 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8214 (mm) REVERT: B 441 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.6872 (t-170) REVERT: C 457 ASP cc_start: 0.8937 (t70) cc_final: 0.8589 (t70) REVERT: C 463 ASN cc_start: 0.9201 (t0) cc_final: 0.8824 (t0) REVERT: C 512 MET cc_start: 0.3331 (mmt) cc_final: 0.2893 (mmt) REVERT: C 572 LYS cc_start: 0.9064 (tptp) cc_final: 0.8653 (tttt) REVERT: C 583 ARG cc_start: 0.9437 (tpp-160) cc_final: 0.9143 (mmm160) REVERT: D 38 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8019 (mt-10) REVERT: D 39 ARG cc_start: 0.9008 (ttp80) cc_final: 0.8799 (ttp80) REVERT: D 105 MET cc_start: 0.1235 (tpt) cc_final: 0.0245 (ptm) outliers start: 49 outliers final: 41 residues processed: 126 average time/residue: 0.2881 time to fit residues: 52.0130 Evaluate side-chains 127 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 84 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 47 LYS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 151 optimal weight: 40.0000 chunk 139 optimal weight: 30.0000 chunk 120 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 overall best weight: 3.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12813 Z= 0.212 Angle : 0.611 11.687 17239 Z= 0.314 Chirality : 0.041 0.258 1894 Planarity : 0.004 0.075 2194 Dihedral : 8.271 87.556 1741 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 22.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.17 % Allowed : 16.71 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.22), residues: 1524 helix: 0.54 (0.21), residues: 619 sheet: 0.09 (0.38), residues: 201 loop : -0.70 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 7 HIS 0.006 0.001 HIS C 477 PHE 0.023 0.001 PHE D 124 TYR 0.016 0.001 TYR A 372 ARG 0.004 0.000 ARG A 638 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3048 Ramachandran restraints generated. 1524 Oldfield, 0 Emsley, 1524 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 85 time to evaluate : 1.667 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: A 125 MET cc_start: 0.7972 (mmm) cc_final: 0.7353 (mmp) REVERT: A 512 MET cc_start: 0.7896 (mmm) cc_final: 0.6988 (mmm) REVERT: B 125 MET cc_start: 0.8351 (mmm) cc_final: 0.7935 (mmm) REVERT: B 193 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8206 (mm) REVERT: B 441 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.6803 (t-170) REVERT: C 457 ASP cc_start: 0.8937 (t70) cc_final: 0.8589 (t70) REVERT: C 463 ASN cc_start: 0.9211 (t0) cc_final: 0.8837 (t0) REVERT: C 512 MET cc_start: 0.3199 (mmt) cc_final: 0.2694 (mmt) REVERT: C 572 LYS cc_start: 0.9058 (tptp) cc_final: 0.8654 (tttt) REVERT: C 583 ARG cc_start: 0.9452 (tpp-160) cc_final: 0.9161 (mmm160) REVERT: D 38 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8087 (mt-10) REVERT: D 39 ARG cc_start: 0.8997 (ttp80) cc_final: 0.8789 (ttp80) REVERT: D 105 MET cc_start: 0.1090 (tpt) cc_final: 0.0189 (ptm) outliers start: 44 outliers final: 40 residues processed: 119 average time/residue: 0.3024 time to fit residues: 51.4953 Evaluate side-chains 127 residues out of total 1388 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 85 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 151 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 426 LYS Chi-restraints excluded: chain A residue 458 THR Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 505 ARG Chi-restraints excluded: chain A residue 542 LEU Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 624 HIS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 156 MET Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 275 TYR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 441 HIS Chi-restraints excluded: chain B residue 456 TYR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 545 ASP Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain C residue 456 MET Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 516 VAL Chi-restraints excluded: chain C residue 553 ASN Chi-restraints excluded: chain C residue 613 LEU Chi-restraints excluded: chain D residue 6 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 22 ASN Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 10.0000 chunk 111 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 124 optimal weight: 0.0670 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.7840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.053400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.039990 restraints weight = 120860.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.040726 restraints weight = 90264.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.041208 restraints weight = 74850.361| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12813 Z= 0.149 Angle : 0.576 11.833 17239 Z= 0.293 Chirality : 0.040 0.267 1894 Planarity : 0.004 0.073 2194 Dihedral : 8.017 89.327 1741 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.74 % Allowed : 17.00 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1524 helix: 0.64 (0.21), residues: 622 sheet: 0.45 (0.37), residues: 213 loop : -0.64 (0.25), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 7 HIS 0.004 0.001 HIS B 314 PHE 0.010 0.001 PHE A 328 TYR 0.013 0.001 TYR B 428 ARG 0.003 0.000 ARG A 638 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2453.67 seconds wall clock time: 46 minutes 20.47 seconds (2780.47 seconds total)