Starting phenix.real_space_refine on Thu Mar 14 21:47:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/03_2024/6xlc_22239_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/03_2024/6xlc_22239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/03_2024/6xlc_22239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/03_2024/6xlc_22239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/03_2024/6xlc_22239_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xlc_22239/03_2024/6xlc_22239_updated.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 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 6 5.49 5 Mg 2 5.21 5 S 18 5.16 5 C 6286 2.51 5 N 1620 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 7": "OE1" <-> "OE2" Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 11": "OE1" <-> "OE2" Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ASP 40": "OD1" <-> "OD2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A ASP 143": "OD1" <-> "OD2" Residue "A PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A GLU 186": "OE1" <-> "OE2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 448": "OD1" <-> "OD2" Residue "A ASP 455": "OD1" <-> "OD2" Residue "A GLU 462": "OE1" <-> "OE2" Residue "A TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 513": "OE1" <-> "OE2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 525": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A ASP 530": "OD1" <-> "OD2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 535": "OE1" <-> "OE2" Residue "A ARG 536": "NH1" <-> "NH2" Residue "A GLU 539": "OE1" <-> "OE2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 587": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A GLU 610": "OE1" <-> "OE2" Residue "A GLU 644": "OE1" <-> "OE2" Residue "A GLU 656": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 11": "OE1" <-> "OE2" Residue "B TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B ASP 132": "OD1" <-> "OD2" Residue "B ARG 133": "NH1" <-> "NH2" Residue "B PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B ASP 295": "OD1" <-> "OD2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 376": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 462": "OE1" <-> "OE2" Residue "B TYR 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 469": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 496": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 502": "OD1" <-> "OD2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 523": "OD1" <-> "OD2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 525": "OE1" <-> "OE2" Residue "B ASP 530": "OD1" <-> "OD2" Residue "B ARG 536": "NH1" <-> "NH2" Residue "B ASP 552": "OD1" <-> "OD2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 587": "NH1" <-> "NH2" Residue "B ARG 595": "NH1" <-> "NH2" Residue "B PHE 609": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 610": "OE1" <-> "OE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 656": "OE1" <-> "OE2" Residue "B PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9858 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "B" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 606, 4897 Classifications: {'peptide': 606} Link IDs: {'PTRANS': 20, 'TRANS': 585} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 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, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.00, per 1000 atoms: 0.51 Number of scatterers: 9858 At special positions: 0 Unit cell: (98.487, 92.133, 131.316, 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 18 16.00 P 6 15.00 Mg 2 11.99 O 1926 8.00 N 1620 7.00 C 6286 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: 3.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2324 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 9 sheets defined 37.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 12 through 19 removed outlier: 4.074A pdb=" N SER A 17 " --> pdb=" O THR A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 51 removed outlier: 3.626A pdb=" N LEU A 31 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN A 48 " --> pdb=" O ILE A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 56 Processing helix chain 'A' and resid 88 through 91 No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 124 through 129 removed outlier: 3.566A pdb=" N LEU A 127 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A 128 " --> pdb=" O TYR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 187 through 196 Processing helix chain 'A' and resid 277 through 279 No H-bonds generated for 'chain 'A' and resid 277 through 279' Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 385 through 405 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 432 through 438 removed outlier: 3.834A pdb=" N LYS A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 Processing helix chain 'A' and resid 475 through 478 No H-bonds generated for 'chain 'A' and resid 475 through 478' Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 502 through 509 removed outlier: 4.033A pdb=" N GLN A 508 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 540 removed outlier: 3.892A pdb=" N GLU A 535 " --> pdb=" O GLU A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 583 through 591 removed outlier: 3.899A pdb=" N ARG A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 616 through 626 removed outlier: 3.712A pdb=" N LYS A 623 " --> pdb=" O LYS A 619 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG A 624 " --> pdb=" O GLU A 620 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 625 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP A 626 " --> pdb=" O LYS A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 650 removed outlier: 3.946A pdb=" N ASP A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 638 " --> pdb=" O THR A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 657 through 671 Processing helix chain 'B' and resid 12 through 21 removed outlier: 4.447A pdb=" N SER B 17 " --> pdb=" O THR B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 51 removed outlier: 4.072A pdb=" N SER B 51 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 56 Processing helix chain 'B' and resid 88 through 91 No H-bonds generated for 'chain 'B' and resid 88 through 91' Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 123 through 129 removed outlier: 3.521A pdb=" N LEU B 127 " --> pdb=" O PHE B 124 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE B 128 " --> pdb=" O TYR B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 185 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 282 through 292 Processing helix chain 'B' and resid 384 through 405 Processing helix chain 'B' and resid 408 through 416 Processing helix chain 'B' and resid 418 through 426 Processing helix chain 'B' and resid 432 through 438 removed outlier: 3.790A pdb=" N LYS B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU B 438 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.603A pdb=" N THR B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 479 Processing helix chain 'B' and resid 485 through 489 Processing helix chain 'B' and resid 502 through 509 removed outlier: 4.009A pdb=" N GLN B 508 " --> pdb=" O TYR B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 540 Processing helix chain 'B' and resid 544 through 554 Processing helix chain 'B' and resid 583 through 591 removed outlier: 3.823A pdb=" N ARG B 587 " --> pdb=" O ALA B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 626 removed outlier: 3.573A pdb=" N LYS B 623 " --> pdb=" O LYS B 619 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 624 " --> pdb=" O GLU B 620 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 625 " --> pdb=" O LEU B 621 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP B 626 " --> pdb=" O LYS B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.858A pdb=" N ASP B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU B 638 " --> pdb=" O THR B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 657 through 671 Processing sheet with id= A, first strand: chain 'A' and resid 156 through 160 removed outlier: 7.567A pdb=" N PHE A 176 " --> pdb=" O ASP A 132 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N VAL A 134 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG A 174 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 136 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL A 172 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER A 138 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY A 170 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU A 76 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 67 " --> pdb=" O GLU A 76 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILE A 66 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN A 206 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU A 208 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 301 through 307 removed outlier: 3.512A pdb=" N TYR A 301 " --> pdb=" O ILE A 319 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 516 through 519 Processing sheet with id= D, first strand: chain 'A' and resid 561 through 563 removed outlier: 6.446A pdb=" N PHE A 609 " --> pdb=" O VAL A 562 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 157 through 160 removed outlier: 3.750A pdb=" N ARG B 174 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE B 66 " --> pdb=" O PRO B 204 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N GLN B 206 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 208 " --> pdb=" O PRO B 68 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 301 through 307 removed outlier: 3.515A pdb=" N VAL B 364 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR B 347 " --> pdb=" O LEU B 339 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL B 341 " --> pdb=" O PHE B 345 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N PHE B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 516 through 519 Processing sheet with id= H, first strand: chain 'B' and resid 561 through 564 removed outlier: 8.947A pdb=" N VAL B 562 " --> pdb=" O LYS B 607 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N PHE B 609 " --> pdb=" O VAL B 562 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N SER B 564 " --> pdb=" O PHE B 609 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE B 611 " --> pdb=" O SER B 564 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 131 through 134 removed outlier: 7.235A pdb=" N PHE B 176 " --> pdb=" O ASP B 132 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3212 1.34 - 1.46: 1542 1.46 - 1.57: 5220 1.57 - 1.69: 10 1.69 - 1.80: 38 Bond restraints: 10022 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" O5' ANP B 801 " pdb=" PA ANP B 801 " ideal model delta sigma weight residual 1.655 1.582 0.073 2.00e-02 2.50e+03 1.35e+01 ... (remaining 10017 not shown) Histogram of bond angle deviations from ideal: 100.28 - 107.01: 217 107.01 - 113.75: 5595 113.75 - 120.49: 4035 120.49 - 127.23: 3610 127.23 - 133.97: 69 Bond angle restraints: 13526 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 109.63 17.32 3.00e+00 1.11e-01 3.33e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 109.73 17.22 3.00e+00 1.11e-01 3.30e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.60 10.48 3.00e+00 1.11e-01 1.22e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.69 10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" N ILE A 20 " pdb=" CA ILE A 20 " pdb=" C ILE A 20 " ideal model delta sigma weight residual 113.71 110.65 3.06 9.50e-01 1.11e+00 1.04e+01 ... (remaining 13521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 5759 17.80 - 35.60: 330 35.60 - 53.39: 67 53.39 - 71.19: 21 71.19 - 88.99: 15 Dihedral angle restraints: 6192 sinusoidal: 2628 harmonic: 3564 Sorted by residual: dihedral pdb=" CB GLU B 76 " pdb=" CG GLU B 76 " pdb=" CD GLU B 76 " pdb=" OE1 GLU B 76 " ideal model delta sinusoidal sigma weight residual 0.00 -88.99 88.99 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU B 513 " pdb=" CG GLU B 513 " pdb=" CD GLU B 513 " pdb=" OE1 GLU B 513 " ideal model delta sinusoidal sigma weight residual 0.00 88.90 -88.90 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" O1B ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PB ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sinusoidal sigma weight residual 35.15 -53.13 88.28 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 6189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1325 0.055 - 0.109: 188 0.109 - 0.164: 19 0.164 - 0.218: 0 0.218 - 0.273: 2 Chirality restraints: 1534 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CA ILE B 77 " pdb=" N ILE B 77 " pdb=" C ILE B 77 " pdb=" CB ILE B 77 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 1531 not shown) Planarity restraints: 1724 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 354 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO A 355 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 20 " -0.005 2.00e-02 2.50e+03 9.43e-03 8.90e-01 pdb=" C ILE A 20 " 0.016 2.00e-02 2.50e+03 pdb=" O ILE A 20 " -0.006 2.00e-02 2.50e+03 pdb=" N ASN A 21 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 543 " 0.005 2.00e-02 2.50e+03 6.32e-03 8.00e-01 pdb=" CG TYR B 543 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 543 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR B 543 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 543 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 543 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 543 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 543 " -0.000 2.00e-02 2.50e+03 ... (remaining 1721 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 133 2.64 - 3.21: 8727 3.21 - 3.77: 15224 3.77 - 4.34: 21757 4.34 - 4.90: 34930 Nonbonded interactions: 80771 Sorted by model distance: nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.079 2.170 nonbonded pdb=" O1B ANP A 801 " pdb="MG MG A 802 " model vdw 2.089 2.170 nonbonded pdb=" O1A ANP B 801 " pdb="MG MG B 802 " model vdw 2.249 2.170 nonbonded pdb=" OD1 ASN B 37 " pdb="MG MG B 802 " model vdw 2.250 2.170 nonbonded pdb=" OH TYR B 456 " pdb=" O GLU B 493 " model vdw 2.255 2.440 ... (remaining 80766 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: 1.250 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: 4.370 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.930 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.144 10022 Z= 0.238 Angle : 0.523 17.324 13526 Z= 0.249 Chirality : 0.039 0.273 1534 Planarity : 0.002 0.029 1724 Dihedral : 12.917 88.987 3868 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.20), residues: 1196 helix: -1.88 (0.19), residues: 492 sheet: -0.99 (0.34), residues: 218 loop : -1.87 (0.23), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 273 HIS 0.001 0.000 HIS A 197 PHE 0.006 0.001 PHE A 652 TYR 0.016 0.001 TYR B 543 ARG 0.001 0.000 ARG B 440 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6542 (mm-30) REVERT: A 610 GLU cc_start: 0.7411 (mp0) cc_final: 0.7104 (mp0) REVERT: A 614 LYS cc_start: 0.6948 (pttm) cc_final: 0.6537 (ptmm) REVERT: B 379 LEU cc_start: 0.5857 (pt) cc_final: 0.5552 (pp) REVERT: B 386 LYS cc_start: 0.6026 (mmtm) cc_final: 0.5820 (tptp) outliers start: 0 outliers final: 0 residues processed: 267 average time/residue: 0.2730 time to fit residues: 95.4894 Evaluate side-chains 146 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 146 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 7.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 91 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 431 ASN A 442 ASN A 592 GLN A 673 ASN ** B 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 420 ASN B 431 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 10022 Z= 0.301 Angle : 0.658 8.263 13526 Z= 0.342 Chirality : 0.045 0.161 1534 Planarity : 0.005 0.036 1724 Dihedral : 6.540 78.646 1358 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.21 % Allowed : 12.64 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.22), residues: 1196 helix: -0.89 (0.22), residues: 496 sheet: -0.79 (0.35), residues: 208 loop : -1.66 (0.23), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 357 HIS 0.004 0.001 HIS B 426 PHE 0.020 0.002 PHE B 652 TYR 0.016 0.002 TYR B 125 ARG 0.005 0.001 ARG B 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 144 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6968 (mm-30) REVERT: A 610 GLU cc_start: 0.7831 (mp0) cc_final: 0.7626 (mt-10) REVERT: B 205 ILE cc_start: 0.7223 (mm) cc_final: 0.6900 (mt) outliers start: 24 outliers final: 12 residues processed: 146 average time/residue: 0.2320 time to fit residues: 47.0957 Evaluate side-chains 102 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASN Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 441 TYR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 611 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 117 optimal weight: 0.8980 chunk 97 optimal weight: 0.1980 chunk 108 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10022 Z= 0.150 Angle : 0.487 6.453 13526 Z= 0.248 Chirality : 0.041 0.160 1534 Planarity : 0.003 0.038 1724 Dihedral : 6.173 77.434 1358 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.29 % Allowed : 15.22 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.23), residues: 1196 helix: -0.31 (0.24), residues: 498 sheet: -0.69 (0.34), residues: 218 loop : -1.36 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 148 HIS 0.003 0.001 HIS B 426 PHE 0.010 0.001 PHE B 124 TYR 0.019 0.001 TYR A 47 ARG 0.005 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 109 time to evaluate : 1.050 Fit side-chains REVERT: A 546 LEU cc_start: 0.6355 (tp) cc_final: 0.6027 (tt) REVERT: B 205 ILE cc_start: 0.7351 (mm) cc_final: 0.6900 (mt) REVERT: B 553 ILE cc_start: 0.7932 (mm) cc_final: 0.7596 (mm) outliers start: 14 outliers final: 9 residues processed: 118 average time/residue: 0.2247 time to fit residues: 37.2528 Evaluate side-chains 86 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 164 ASN Chi-restraints excluded: chain B residue 339 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 12 optimal weight: 0.4980 chunk 52 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 115 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 31 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10022 Z= 0.132 Angle : 0.460 6.736 13526 Z= 0.235 Chirality : 0.040 0.161 1534 Planarity : 0.003 0.038 1724 Dihedral : 6.006 78.164 1358 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.75 % Allowed : 16.05 % Favored : 82.20 % 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: -0.84 (0.24), residues: 1196 helix: 0.08 (0.24), residues: 494 sheet: -0.46 (0.34), residues: 218 loop : -1.15 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 148 HIS 0.003 0.001 HIS B 426 PHE 0.014 0.001 PHE B 6 TYR 0.018 0.001 TYR A 47 ARG 0.004 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 94 time to evaluate : 0.952 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8187 (pp20) cc_final: 0.7151 (pp20) REVERT: A 537 GLU cc_start: 0.7489 (mm-30) cc_final: 0.7269 (mm-30) REVERT: A 589 MET cc_start: 0.7524 (mmt) cc_final: 0.7280 (mmt) REVERT: B 116 MET cc_start: 0.6881 (mtt) cc_final: 0.6569 (mtt) REVERT: B 205 ILE cc_start: 0.7296 (mm) cc_final: 0.7055 (mt) REVERT: B 339 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8524 (tt) outliers start: 19 outliers final: 12 residues processed: 106 average time/residue: 0.1966 time to fit residues: 31.3287 Evaluate side-chains 89 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 474 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 5.9990 chunk 65 optimal weight: 0.2980 chunk 1 optimal weight: 0.0030 chunk 86 optimal weight: 20.0000 chunk 47 optimal weight: 9.9990 chunk 98 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 0.0170 overall best weight: 0.4428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10022 Z= 0.124 Angle : 0.450 9.092 13526 Z= 0.229 Chirality : 0.040 0.157 1534 Planarity : 0.003 0.036 1724 Dihedral : 5.908 78.847 1358 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.85 % Allowed : 16.97 % Favored : 81.18 % 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: -0.43 (0.24), residues: 1196 helix: 0.42 (0.25), residues: 486 sheet: -0.39 (0.37), residues: 196 loop : -0.81 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 148 HIS 0.002 0.001 HIS B 426 PHE 0.035 0.001 PHE B 124 TYR 0.014 0.001 TYR A 47 ARG 0.005 0.000 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 1.186 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.6976 (mpp) cc_final: 0.6711 (mtt) REVERT: B 116 MET cc_start: 0.6834 (mtt) cc_final: 0.6581 (mtt) REVERT: B 339 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8503 (tt) REVERT: B 343 ARG cc_start: 0.6932 (mmm-85) cc_final: 0.6651 (ptp-110) REVERT: B 553 ILE cc_start: 0.7569 (mm) cc_final: 0.7213 (mm) outliers start: 20 outliers final: 15 residues processed: 112 average time/residue: 0.1912 time to fit residues: 32.3538 Evaluate side-chains 91 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 339 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 2.9990 chunk 104 optimal weight: 0.5980 chunk 22 optimal weight: 0.0670 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 7.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10022 Z= 0.137 Angle : 0.461 6.585 13526 Z= 0.238 Chirality : 0.040 0.156 1534 Planarity : 0.003 0.034 1724 Dihedral : 5.801 70.315 1358 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.40 % Allowed : 16.97 % Favored : 80.63 % 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: -0.28 (0.24), residues: 1196 helix: 0.51 (0.25), residues: 486 sheet: -0.28 (0.38), residues: 196 loop : -0.72 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 148 HIS 0.001 0.000 HIS A 197 PHE 0.018 0.001 PHE B 124 TYR 0.007 0.001 TYR A 47 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8180 (pp20) cc_final: 0.7075 (pp20) REVERT: A 116 MET cc_start: 0.7058 (mpp) cc_final: 0.6787 (mtt) REVERT: A 560 LYS cc_start: 0.7356 (ptmt) cc_final: 0.7112 (ttpt) REVERT: A 664 ILE cc_start: 0.8054 (mt) cc_final: 0.7375 (mm) REVERT: B 116 MET cc_start: 0.6895 (mtt) cc_final: 0.6655 (mtt) REVERT: B 205 ILE cc_start: 0.7279 (mm) cc_final: 0.6971 (mt) REVERT: B 322 ARG cc_start: 0.5346 (ppt170) cc_final: 0.4919 (ttt180) REVERT: B 339 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8534 (tt) REVERT: B 553 ILE cc_start: 0.7508 (mm) cc_final: 0.7127 (mm) outliers start: 26 outliers final: 17 residues processed: 115 average time/residue: 0.1970 time to fit residues: 33.4187 Evaluate side-chains 91 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 73 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain B residue 339 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 0.0370 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 97 optimal weight: 0.2980 chunk 64 optimal weight: 1.9990 chunk 115 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 overall best weight: 1.8664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 420 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10022 Z= 0.250 Angle : 0.565 10.121 13526 Z= 0.289 Chirality : 0.043 0.152 1534 Planarity : 0.004 0.042 1724 Dihedral : 6.140 66.341 1358 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.03 % Allowed : 18.91 % Favored : 79.06 % 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: -0.55 (0.24), residues: 1196 helix: 0.23 (0.24), residues: 482 sheet: -0.28 (0.38), residues: 196 loop : -0.85 (0.26), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 581 HIS 0.002 0.000 HIS A 426 PHE 0.019 0.002 PHE B 124 TYR 0.015 0.001 TYR B 125 ARG 0.004 0.000 ARG A 432 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 85 time to evaluate : 1.274 Fit side-chains revert: symmetry clash REVERT: A 116 MET cc_start: 0.7091 (mpp) cc_final: 0.6756 (mtt) REVERT: B 205 ILE cc_start: 0.7336 (mm) cc_final: 0.6834 (mt) REVERT: B 322 ARG cc_start: 0.5557 (ppt170) cc_final: 0.4694 (ptm160) REVERT: B 553 ILE cc_start: 0.7980 (mm) cc_final: 0.7488 (mm) outliers start: 22 outliers final: 20 residues processed: 103 average time/residue: 0.2022 time to fit residues: 31.0403 Evaluate side-chains 92 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 526 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 4.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.3980 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.7364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10022 Z= 0.151 Angle : 0.507 7.570 13526 Z= 0.259 Chirality : 0.041 0.155 1534 Planarity : 0.003 0.041 1724 Dihedral : 6.006 71.905 1358 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.66 % Allowed : 20.30 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1196 helix: 0.20 (0.24), residues: 494 sheet: -0.25 (0.39), residues: 196 loop : -0.76 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 148 HIS 0.001 0.000 HIS A 197 PHE 0.017 0.001 PHE B 124 TYR 0.009 0.001 TYR B 125 ARG 0.005 0.000 ARG B 536 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.183 Fit side-chains revert: symmetry clash REVERT: A 560 LYS cc_start: 0.7646 (ptmt) cc_final: 0.7309 (ttpt) REVERT: B 205 ILE cc_start: 0.7351 (mm) cc_final: 0.6978 (mt) REVERT: B 322 ARG cc_start: 0.5409 (ppt170) cc_final: 0.5115 (ttt180) REVERT: B 553 ILE cc_start: 0.7464 (mm) cc_final: 0.7095 (mm) outliers start: 18 outliers final: 16 residues processed: 97 average time/residue: 0.1875 time to fit residues: 27.6399 Evaluate side-chains 84 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 68 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 526 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 7.9990 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.7581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10022 Z= 0.155 Angle : 0.497 7.294 13526 Z= 0.255 Chirality : 0.041 0.157 1534 Planarity : 0.003 0.043 1724 Dihedral : 5.939 64.737 1358 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.94 % Allowed : 20.66 % Favored : 77.40 % 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: -0.37 (0.25), residues: 1196 helix: 0.32 (0.24), residues: 490 sheet: -0.33 (0.39), residues: 200 loop : -0.64 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 148 HIS 0.001 0.000 HIS A 197 PHE 0.012 0.001 PHE B 579 TYR 0.010 0.001 TYR B 125 ARG 0.008 0.000 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 1.220 Fit side-chains REVERT: A 560 LYS cc_start: 0.7601 (ptmt) cc_final: 0.7377 (ttpt) REVERT: B 322 ARG cc_start: 0.5456 (ppt170) cc_final: 0.5235 (ttt180) REVERT: B 553 ILE cc_start: 0.7503 (mm) cc_final: 0.7139 (mm) outliers start: 21 outliers final: 18 residues processed: 98 average time/residue: 0.2052 time to fit residues: 29.5677 Evaluate side-chains 89 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 339 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.5980 chunk 79 optimal weight: 0.6980 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 101 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.7992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10022 Z= 0.234 Angle : 0.576 8.056 13526 Z= 0.294 Chirality : 0.042 0.165 1534 Planarity : 0.004 0.047 1724 Dihedral : 6.162 61.909 1358 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.12 % Allowed : 20.11 % Favored : 77.77 % 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: -0.42 (0.25), residues: 1196 helix: 0.30 (0.25), residues: 484 sheet: -0.27 (0.39), residues: 196 loop : -0.72 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 581 HIS 0.001 0.000 HIS A 426 PHE 0.011 0.002 PHE B 313 TYR 0.012 0.001 TYR B 125 ARG 0.009 0.001 ARG B 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2392 Ramachandran restraints generated. 1196 Oldfield, 0 Emsley, 1196 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 73 time to evaluate : 1.260 Fit side-chains REVERT: B 205 ILE cc_start: 0.7289 (mm) cc_final: 0.6785 (mt) REVERT: B 553 ILE cc_start: 0.7601 (mm) cc_final: 0.7243 (mm) outliers start: 23 outliers final: 18 residues processed: 93 average time/residue: 0.1779 time to fit residues: 25.6720 Evaluate side-chains 83 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 65 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ILE Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 147 ILE Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 499 ASP Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 576 THR Chi-restraints excluded: chain A residue 584 ASN Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 526 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 68 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 ASN ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.122509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.107932 restraints weight = 20513.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.110876 restraints weight = 12055.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.112920 restraints weight = 8239.050| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.8200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10022 Z= 0.208 Angle : 0.550 7.474 13526 Z= 0.282 Chirality : 0.042 0.218 1534 Planarity : 0.004 0.046 1724 Dihedral : 6.178 65.043 1358 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.66 % Allowed : 20.66 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.25), residues: 1196 helix: 0.31 (0.24), residues: 484 sheet: -0.26 (0.39), residues: 196 loop : -0.71 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 581 HIS 0.001 0.000 HIS A 426 PHE 0.016 0.001 PHE B 124 TYR 0.008 0.001 TYR A 289 ARG 0.009 0.000 ARG B 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.29 seconds wall clock time: 33 minutes 56.43 seconds (2036.43 seconds total)