Starting phenix.real_space_refine on Thu Feb 15 07:30:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoa_28332/02_2024/8eoa_28332_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoa_28332/02_2024/8eoa_28332.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoa_28332/02_2024/8eoa_28332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoa_28332/02_2024/8eoa_28332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoa_28332/02_2024/8eoa_28332_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoa_28332/02_2024/8eoa_28332_updated.pdb" } resolution = 3.9 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= -0.007 sd= 0.728 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 56 5.16 5 C 7298 2.51 5 N 1939 2.21 5 O 2234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11535 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 629, 5092 Classifications: {'peptide': 629} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 611} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 5072 Classifications: {'peptide': 627} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 17, 'TRANS': 609} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1307 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 7, 'TRANS': 157} 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} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ASP C 7 " occ=0.93 ... (6 atoms not shown) pdb=" OD2 ASP C 7 " occ=0.93 residue: pdb=" N LEU C 10 " occ=0.93 ... (6 atoms not shown) pdb=" CD2 LEU C 10 " occ=0.93 residue: pdb=" N LEU C 11 " occ=0.93 ... (6 atoms not shown) pdb=" CD2 LEU C 11 " occ=0.93 residue: pdb=" N LEU C 12 " occ=0.93 ... (6 atoms not shown) pdb=" CD2 LEU C 12 " occ=0.93 Time building chain proxies: 6.32, per 1000 atoms: 0.55 Number of scatterers: 11535 At special positions: 0 Unit cell: (94.848, 114.816, 131.04, 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 56 16.00 P 6 15.00 Mg 2 11.99 O 2234 8.00 N 1939 7.00 C 7298 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: 4.27 Conformation dependent library (CDL) restraints added in 2.1 seconds 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 11 sheets defined 38.1% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 36 through 59 removed outlier: 3.771A pdb=" N PHE A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU A 40 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A 44 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 398 through 421 removed outlier: 4.164A pdb=" N GLU A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 443 removed outlier: 6.466A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 454 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 501 through 505 Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.730A pdb=" N GLN A 524 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 570 removed outlier: 3.576A pdb=" N GLU A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ASN A 562 " --> pdb=" O ALA A 558 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU A 563 " --> pdb=" O LYS A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.733A pdb=" N GLY A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 619' Processing helix chain 'A' and resid 633 through 644 Processing helix chain 'A' and resid 649 through 665 Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 21 through 31 Processing helix chain 'B' and resid 36 through 59 removed outlier: 3.797A pdb=" N PHE B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU B 40 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE B 44 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 132 through 138 Processing helix chain 'B' and resid 191 through 193 No H-bonds generated for 'chain 'B' and resid 191 through 193' Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 398 through 421 removed outlier: 4.431A pdb=" N GLU B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 443 removed outlier: 6.444A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 removed outlier: 4.297A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.018A pdb=" N ARG B 502 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL B 503 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG B 504 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 3.609A pdb=" N GLN B 524 " --> pdb=" O CYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 570 removed outlier: 5.397A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.274A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 617 through 620 No H-bonds generated for 'chain 'B' and resid 617 through 620' Processing helix chain 'B' and resid 633 through 644 Processing helix chain 'B' and resid 649 through 666 Processing helix chain 'B' and resid 673 through 688 Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 75 through 82 removed outlier: 3.689A pdb=" N THR C 82 " --> pdb=" O GLU C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 111 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 140 through 146 Processing sheet with id= A, first strand: chain 'A' and resid 212 through 216 removed outlier: 3.657A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 217 through 219 Processing sheet with id= C, first strand: chain 'A' and resid 353 through 357 removed outlier: 7.569A pdb=" N LYS A 354 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N GLY A 379 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N TYR A 356 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL A 381 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.064A pdb=" N VAL A 511 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 577 through 580 Processing sheet with id= F, first strand: chain 'B' and resid 276 through 281 removed outlier: 6.021A pdb=" N ILE B 73 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N TYR B 216 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE B 75 " --> pdb=" O TYR B 216 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N GLU B 218 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS B 142 " --> pdb=" O HIS B 184 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 361 through 364 removed outlier: 7.114A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ASP B 364 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE B 353 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY B 379 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N TYR B 356 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N VAL B 381 " --> pdb=" O TYR B 356 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 532 through 535 Processing sheet with id= I, first strand: chain 'B' and resid 577 through 580 Processing sheet with id= J, first strand: chain 'C' and resid 17 through 21 removed outlier: 3.805A pdb=" N LEU C 152 " --> pdb=" O CYS C 94 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 153 " --> pdb=" O MET C 45 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR C 39 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL C 161 " --> pdb=" O ARG C 37 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ARG C 37 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 43 through 45 460 hydrogen bonds defined for protein. 1173 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: 3.49 Time building geometry restraints manager: 4.60 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: 3772 1.34 - 1.46: 2432 1.46 - 1.58: 5426 1.58 - 1.69: 8 1.69 - 1.81: 97 Bond restraints: 11735 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.86e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.573 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 11730 not shown) Histogram of bond angle deviations from ideal: 99.37 - 106.32: 257 106.32 - 113.26: 6496 113.26 - 120.21: 4116 120.21 - 127.16: 4842 127.16 - 134.10: 93 Bond angle restraints: 15804 Sorted by residual: angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 108.41 18.54 3.00e+00 1.11e-01 3.82e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.11 16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C ASN B 46 " pdb=" CA ASN B 46 " pdb=" CB ASN B 46 " ideal model delta sigma weight residual 110.92 105.37 5.55 1.59e+00 3.96e-01 1.22e+01 angle pdb=" N ASN B 46 " pdb=" CA ASN B 46 " pdb=" C ASN B 46 " ideal model delta sigma weight residual 111.02 107.02 4.00 1.22e+00 6.72e-01 1.08e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 110.25 9.83 3.00e+00 1.11e-01 1.07e+01 ... (remaining 15799 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 7164 34.84 - 69.68: 74 69.68 - 104.52: 5 104.52 - 139.35: 0 139.35 - 174.19: 1 Dihedral angle restraints: 7244 sinusoidal: 3081 harmonic: 4163 Sorted by residual: dihedral pdb=" O1B ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PB ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sinusoidal sigma weight residual 35.15 -150.66 -174.19 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C ASN B 46 " pdb=" N ASN B 46 " pdb=" CA ASN B 46 " pdb=" CB ASN B 46 " ideal model delta harmonic sigma weight residual -122.60 -114.21 -8.39 0 2.50e+00 1.60e-01 1.13e+01 dihedral pdb=" CA ALA C 133 " pdb=" C ALA C 133 " pdb=" N TYR C 134 " pdb=" CA TYR C 134 " ideal model delta harmonic sigma weight residual -180.00 -163.98 -16.02 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 7241 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1520 0.056 - 0.112: 223 0.112 - 0.168: 13 0.168 - 0.224: 0 0.224 - 0.280: 3 Chirality restraints: 1759 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 -2.64 0.28 2.00e-01 2.50e+01 1.96e+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 1.80e+00 chirality pdb=" CA ASN B 46 " pdb=" N ASN B 46 " pdb=" C ASN B 46 " pdb=" CB ASN B 46 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 1756 not shown) Planarity restraints: 2011 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 370 " -0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO B 371 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 517 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.99e+00 pdb=" C ILE A 517 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 517 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 518 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 370 " 0.028 5.00e-02 4.00e+02 4.27e-02 2.92e+00 pdb=" N PRO A 371 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " 0.024 5.00e-02 4.00e+02 ... (remaining 2008 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 17 2.35 - 2.99: 6323 2.99 - 3.63: 16936 3.63 - 4.26: 25373 4.26 - 4.90: 42634 Nonbonded interactions: 91283 Sorted by model distance: nonbonded pdb=" O2A ANP A 801 " pdb="MG MG A 802 " model vdw 1.718 2.170 nonbonded pdb=" N3B ANP A 801 " pdb="MG MG A 802 " model vdw 1.887 2.250 nonbonded pdb=" PG ANP A 801 " pdb="MG MG A 802 " model vdw 2.112 2.530 nonbonded pdb=" N3B ANP A 801 " pdb=" O2A ANP A 801 " model vdw 2.122 2.520 nonbonded pdb=" O3G ANP A 801 " pdb="MG MG A 802 " model vdw 2.125 2.170 ... (remaining 91278 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' and (resid 11 through 220 or resid 275 through 691 or resid 801 throu \ gh 802)) 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=0.00 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: 0.400 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: 2.430 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 32.040 Find NCS groups from input model: 0.620 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 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 : 0.004 0.150 11735 Z= 0.258 Angle : 0.584 18.543 15804 Z= 0.287 Chirality : 0.040 0.280 1759 Planarity : 0.003 0.044 2011 Dihedral : 11.607 174.192 4548 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.64 % Allowed : 7.04 % Favored : 91.32 % 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: 0.27 (0.23), residues: 1411 helix: 1.31 (0.23), residues: 568 sheet: 0.07 (0.33), residues: 258 loop : -0.86 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 312 HIS 0.004 0.001 HIS B 632 PHE 0.009 0.001 PHE A 668 TYR 0.016 0.001 TYR B 211 ARG 0.005 0.000 ARG B 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 366 time to evaluate : 1.285 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 114 MET cc_start: 0.8536 (tpp) cc_final: 0.7945 (tmm) REVERT: A 606 MET cc_start: 0.8543 (ttm) cc_final: 0.8244 (tpp) REVERT: A 611 LEU cc_start: 0.9302 (mm) cc_final: 0.8687 (tp) REVERT: A 621 MET cc_start: 0.8701 (mmm) cc_final: 0.8458 (mmt) REVERT: A 626 LEU cc_start: 0.9202 (tp) cc_final: 0.8961 (tp) REVERT: B 25 MET cc_start: 0.8724 (tpp) cc_final: 0.8415 (tpp) REVERT: B 49 ASP cc_start: 0.8465 (m-30) cc_final: 0.8134 (m-30) REVERT: B 114 MET cc_start: 0.8558 (tpp) cc_final: 0.7980 (tpt) REVERT: B 311 ASP cc_start: 0.8560 (t0) cc_final: 0.8198 (t0) REVERT: B 362 ILE cc_start: 0.9469 (mm) cc_final: 0.9219 (tp) REVERT: B 436 ASN cc_start: 0.9027 (m110) cc_final: 0.8595 (m-40) REVERT: B 564 CYS cc_start: 0.9126 (m) cc_final: 0.8449 (m) REVERT: B 606 MET cc_start: 0.8595 (mmt) cc_final: 0.8312 (mmt) REVERT: B 681 TYR cc_start: 0.8381 (m-10) cc_final: 0.8081 (m-80) REVERT: C 5 HIS cc_start: 0.6998 (m90) cc_final: 0.6354 (m170) REVERT: C 40 PHE cc_start: 0.8601 (p90) cc_final: 0.7880 (p90) REVERT: C 45 MET cc_start: 0.9074 (mpp) cc_final: 0.8498 (mpp) REVERT: C 95 ASP cc_start: 0.8931 (m-30) cc_final: 0.8669 (m-30) REVERT: C 139 TYR cc_start: 0.6492 (OUTLIER) cc_final: 0.5880 (t80) REVERT: C 150 GLN cc_start: 0.7908 (mp10) cc_final: 0.7279 (mp-120) outliers start: 21 outliers final: 6 residues processed: 381 average time/residue: 0.2635 time to fit residues: 137.2614 Evaluate side-chains 222 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 58 optimal weight: 30.0000 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 42 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 HIS ** A 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 GLN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 352 ASN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN C 146 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 11735 Z= 0.357 Angle : 0.677 11.201 15804 Z= 0.352 Chirality : 0.042 0.186 1759 Planarity : 0.004 0.052 2011 Dihedral : 8.200 177.640 1608 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.74 % Allowed : 15.40 % Favored : 81.86 % 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: 0.25 (0.23), residues: 1411 helix: 1.01 (0.23), residues: 556 sheet: 0.31 (0.33), residues: 251 loop : -0.63 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 312 HIS 0.006 0.001 HIS A 315 PHE 0.021 0.002 PHE B 133 TYR 0.018 0.002 TYR B 426 ARG 0.005 0.001 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 198 time to evaluate : 1.588 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 114 MET cc_start: 0.8896 (tpp) cc_final: 0.8603 (tmm) REVERT: A 394 MET cc_start: 0.8651 (ptp) cc_final: 0.8391 (ptm) REVERT: A 513 MET cc_start: 0.8522 (mtt) cc_final: 0.8187 (mtt) REVERT: A 606 MET cc_start: 0.8887 (ttm) cc_final: 0.8622 (tpt) REVERT: B 125 MET cc_start: 0.7090 (mtm) cc_final: 0.6863 (mtm) REVERT: B 311 ASP cc_start: 0.8561 (t0) cc_final: 0.8304 (t0) REVERT: B 436 ASN cc_start: 0.9034 (m110) cc_final: 0.8767 (m110) REVERT: B 553 MET cc_start: 0.8950 (tmm) cc_final: 0.8393 (ppp) REVERT: B 627 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8434 (pm20) REVERT: B 681 TYR cc_start: 0.8573 (m-10) cc_final: 0.8298 (m-80) REVERT: C 45 MET cc_start: 0.9153 (mpp) cc_final: 0.8613 (mpp) REVERT: C 64 MET cc_start: 0.9208 (tmm) cc_final: 0.8716 (tmm) REVERT: C 102 TYR cc_start: 0.8963 (t80) cc_final: 0.8729 (t80) outliers start: 35 outliers final: 26 residues processed: 218 average time/residue: 0.2288 time to fit residues: 73.3053 Evaluate side-chains 193 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 35 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 123 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 487 THR Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 143 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 127 optimal weight: 0.0060 chunk 137 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 overall best weight: 2.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 351 ASN A 523 GLN A 640 GLN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11735 Z= 0.176 Angle : 0.565 8.597 15804 Z= 0.291 Chirality : 0.040 0.152 1759 Planarity : 0.003 0.046 2011 Dihedral : 7.510 168.377 1607 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.50 % Allowed : 17.67 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.23), residues: 1411 helix: 1.02 (0.23), residues: 559 sheet: 0.41 (0.33), residues: 258 loop : -0.70 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 312 HIS 0.008 0.001 HIS C 5 PHE 0.017 0.001 PHE B 133 TYR 0.014 0.001 TYR A 457 ARG 0.004 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 1.241 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 23 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8455 (pm20) REVERT: A 333 LEU cc_start: 0.9249 (mt) cc_final: 0.8926 (mp) REVERT: A 356 TYR cc_start: 0.8603 (m-80) cc_final: 0.8354 (m-80) REVERT: A 476 MET cc_start: 0.8551 (ttt) cc_final: 0.8213 (tmm) REVERT: A 567 MET cc_start: 0.8954 (mmm) cc_final: 0.8665 (mmm) REVERT: A 606 MET cc_start: 0.8780 (ttm) cc_final: 0.7804 (tpp) REVERT: A 621 MET cc_start: 0.8632 (mmm) cc_final: 0.8408 (mpp) REVERT: B 311 ASP cc_start: 0.8478 (t0) cc_final: 0.8231 (t0) REVERT: B 362 ILE cc_start: 0.9432 (mm) cc_final: 0.9087 (tp) REVERT: B 385 ASP cc_start: 0.8743 (t0) cc_final: 0.8392 (p0) REVERT: B 436 ASN cc_start: 0.8939 (m110) cc_final: 0.8537 (m-40) REVERT: B 553 MET cc_start: 0.8984 (tmm) cc_final: 0.8479 (ppp) REVERT: B 627 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8305 (pm20) REVERT: B 681 TYR cc_start: 0.8536 (m-10) cc_final: 0.8305 (m-80) REVERT: C 45 MET cc_start: 0.9176 (mpp) cc_final: 0.8582 (mpp) REVERT: C 84 MET cc_start: 0.8734 (tpp) cc_final: 0.8412 (tpp) REVERT: C 102 TYR cc_start: 0.8875 (t80) cc_final: 0.8630 (t80) REVERT: C 143 ASP cc_start: 0.9666 (m-30) cc_final: 0.9455 (p0) outliers start: 32 outliers final: 16 residues processed: 212 average time/residue: 0.2242 time to fit residues: 69.3097 Evaluate side-chains 187 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 20.0000 chunk 95 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 127 optimal weight: 20.0000 chunk 135 optimal weight: 0.0570 chunk 121 optimal weight: 1.9990 chunk 36 optimal weight: 10.0000 chunk 112 optimal weight: 6.9990 overall best weight: 3.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 GLN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 609 GLN C 146 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11735 Z= 0.218 Angle : 0.595 12.084 15804 Z= 0.301 Chirality : 0.041 0.150 1759 Planarity : 0.003 0.043 2011 Dihedral : 7.469 170.686 1603 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.50 % Allowed : 18.37 % Favored : 79.12 % 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: 0.22 (0.23), residues: 1411 helix: 0.93 (0.23), residues: 557 sheet: 0.50 (0.34), residues: 261 loop : -0.71 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 312 HIS 0.010 0.001 HIS C 5 PHE 0.023 0.001 PHE A 208 TYR 0.017 0.001 TYR B 137 ARG 0.004 0.000 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 1.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8511 (pm20) REVERT: A 476 MET cc_start: 0.8457 (ttt) cc_final: 0.8143 (tmm) REVERT: A 513 MET cc_start: 0.8633 (mtt) cc_final: 0.8430 (mtt) REVERT: A 538 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8816 (mmmm) REVERT: A 567 MET cc_start: 0.9142 (mmm) cc_final: 0.8728 (mmm) REVERT: A 660 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8449 (mt-10) REVERT: B 311 ASP cc_start: 0.8490 (t0) cc_final: 0.8241 (t0) REVERT: B 362 ILE cc_start: 0.9448 (mm) cc_final: 0.9061 (tp) REVERT: B 385 ASP cc_start: 0.8813 (t0) cc_final: 0.8389 (p0) REVERT: B 476 MET cc_start: 0.7769 (ttt) cc_final: 0.7444 (ttt) REVERT: B 553 MET cc_start: 0.8962 (tmm) cc_final: 0.8520 (ppp) REVERT: B 616 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.7635 (p) REVERT: B 627 GLU cc_start: 0.8584 (mt-10) cc_final: 0.8249 (pm20) REVERT: B 681 TYR cc_start: 0.8637 (m-10) cc_final: 0.8332 (m-80) REVERT: C 40 PHE cc_start: 0.9143 (p90) cc_final: 0.8801 (p90) REVERT: C 45 MET cc_start: 0.9146 (mpp) cc_final: 0.8754 (mpp) REVERT: C 72 PHE cc_start: 0.7000 (p90) cc_final: 0.6792 (p90) REVERT: C 75 GLU cc_start: 0.9105 (pp20) cc_final: 0.8371 (mp0) REVERT: C 102 TYR cc_start: 0.8931 (t80) cc_final: 0.8689 (t80) REVERT: C 143 ASP cc_start: 0.9674 (OUTLIER) cc_final: 0.9448 (p0) outliers start: 32 outliers final: 24 residues processed: 200 average time/residue: 0.2046 time to fit residues: 61.4363 Evaluate side-chains 188 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 538 LYS Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 616 THR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 143 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 93 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 10.0000 chunk 45 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 ASN ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 609 GLN ** B 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 11735 Z= 0.427 Angle : 0.719 10.131 15804 Z= 0.375 Chirality : 0.043 0.151 1759 Planarity : 0.004 0.042 2011 Dihedral : 8.010 173.618 1603 Min Nonbonded Distance : 1.749 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.60 % Allowed : 18.61 % Favored : 77.80 % 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: 1411 helix: 0.48 (0.22), residues: 550 sheet: 0.46 (0.34), residues: 248 loop : -0.81 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 289 HIS 0.007 0.001 HIS C 5 PHE 0.020 0.002 PHE B 429 TYR 0.021 0.002 TYR B 137 ARG 0.006 0.001 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 153 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.8518 (pm20) REVERT: A 513 MET cc_start: 0.8605 (mtt) cc_final: 0.8362 (mtt) REVERT: A 567 MET cc_start: 0.9318 (mmm) cc_final: 0.8948 (mmm) REVERT: A 621 MET cc_start: 0.8680 (mmm) cc_final: 0.8346 (mmm) REVERT: B 311 ASP cc_start: 0.8636 (t0) cc_final: 0.8376 (t0) REVERT: B 553 MET cc_start: 0.8897 (tmm) cc_final: 0.8465 (ppp) REVERT: B 627 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8497 (pm20) REVERT: B 681 TYR cc_start: 0.8803 (m-10) cc_final: 0.8547 (m-80) REVERT: C 45 MET cc_start: 0.9150 (mpp) cc_final: 0.8687 (mpp) REVERT: C 84 MET cc_start: 0.8563 (tpp) cc_final: 0.8333 (tpp) REVERT: C 102 TYR cc_start: 0.9067 (t80) cc_final: 0.8787 (t80) outliers start: 46 outliers final: 32 residues processed: 184 average time/residue: 0.1863 time to fit residues: 53.1851 Evaluate side-chains 171 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 138 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 54 ILE Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 584 LEU Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 97 ASP Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 459 THR Chi-restraints excluded: chain B residue 467 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 587 SER Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 139 TYR Chi-restraints excluded: chain C residue 143 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 135 optimal weight: 0.3980 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 0.0570 chunk 11 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11735 Z= 0.151 Angle : 0.624 11.265 15804 Z= 0.311 Chirality : 0.041 0.167 1759 Planarity : 0.003 0.040 2011 Dihedral : 7.313 161.153 1603 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.19 % Allowed : 19.70 % Favored : 78.11 % 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: 0.10 (0.23), residues: 1411 helix: 0.75 (0.23), residues: 555 sheet: 0.75 (0.35), residues: 243 loop : -0.80 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 157 HIS 0.003 0.001 HIS A 676 PHE 0.015 0.001 PHE C 42 TYR 0.014 0.001 TYR A 596 ARG 0.005 0.000 ARG A 679 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 182 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8356 (pm20) REVERT: A 476 MET cc_start: 0.8547 (ttt) cc_final: 0.8335 (tmm) REVERT: A 513 MET cc_start: 0.8337 (mtt) cc_final: 0.8077 (mtt) REVERT: A 567 MET cc_start: 0.9247 (mmm) cc_final: 0.8849 (mmm) REVERT: B 93 MET cc_start: 0.8505 (tmm) cc_final: 0.8271 (tmm) REVERT: B 311 ASP cc_start: 0.8477 (t0) cc_final: 0.8252 (t0) REVERT: B 328 GLU cc_start: 0.8330 (tm-30) cc_final: 0.8113 (tm-30) REVERT: B 362 ILE cc_start: 0.9415 (mm) cc_final: 0.9006 (tp) REVERT: B 385 ASP cc_start: 0.8730 (t0) cc_final: 0.8349 (p0) REVERT: B 513 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7631 (mtm) REVERT: B 553 MET cc_start: 0.8972 (tmm) cc_final: 0.8506 (ppp) REVERT: B 627 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8402 (pm20) REVERT: B 681 TYR cc_start: 0.8678 (m-10) cc_final: 0.8342 (m-80) REVERT: C 45 MET cc_start: 0.9203 (mpp) cc_final: 0.8970 (mpp) REVERT: C 72 PHE cc_start: 0.6841 (p90) cc_final: 0.6614 (p90) REVERT: C 75 GLU cc_start: 0.9085 (pp20) cc_final: 0.8368 (mp0) REVERT: C 84 MET cc_start: 0.8444 (tpp) cc_final: 0.8226 (tpp) REVERT: C 95 ASP cc_start: 0.9078 (m-30) cc_final: 0.8663 (m-30) REVERT: C 102 TYR cc_start: 0.8966 (t80) cc_final: 0.8731 (t80) REVERT: C 139 TYR cc_start: 0.6856 (OUTLIER) cc_final: 0.6175 (t80) REVERT: C 143 ASP cc_start: 0.9653 (m-30) cc_final: 0.9417 (p0) outliers start: 28 outliers final: 13 residues processed: 203 average time/residue: 0.2029 time to fit residues: 62.4079 Evaluate side-chains 171 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 155 time to evaluate : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 601 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 134 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11735 Z= 0.249 Angle : 0.652 11.486 15804 Z= 0.331 Chirality : 0.043 0.268 1759 Planarity : 0.004 0.042 2011 Dihedral : 7.586 172.951 1601 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.19 % Allowed : 20.48 % Favored : 77.33 % 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: -0.06 (0.23), residues: 1411 helix: 0.58 (0.22), residues: 553 sheet: 0.60 (0.34), residues: 251 loop : -0.84 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 289 HIS 0.007 0.001 HIS C 5 PHE 0.021 0.002 PHE C 40 TYR 0.016 0.001 TYR A 373 ARG 0.003 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: A 476 MET cc_start: 0.8640 (ttt) cc_final: 0.8339 (tmm) REVERT: A 513 MET cc_start: 0.8474 (mtt) cc_final: 0.8248 (mtt) REVERT: A 567 MET cc_start: 0.9274 (mmm) cc_final: 0.8904 (mmm) REVERT: B 311 ASP cc_start: 0.8515 (t0) cc_final: 0.8277 (t0) REVERT: B 362 ILE cc_start: 0.9455 (mm) cc_final: 0.9096 (tp) REVERT: B 385 ASP cc_start: 0.8906 (t0) cc_final: 0.8491 (p0) REVERT: B 513 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7673 (mtm) REVERT: B 553 MET cc_start: 0.8946 (tmm) cc_final: 0.8537 (ppp) REVERT: B 602 MET cc_start: 0.8854 (tpp) cc_final: 0.8342 (tpp) REVERT: B 627 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8384 (pm20) REVERT: B 668 PHE cc_start: 0.8519 (m-80) cc_final: 0.8218 (m-10) REVERT: B 681 TYR cc_start: 0.8763 (m-10) cc_final: 0.8420 (m-80) REVERT: C 40 PHE cc_start: 0.9071 (p90) cc_final: 0.8789 (p90) REVERT: C 84 MET cc_start: 0.8465 (tpp) cc_final: 0.8249 (tpp) REVERT: C 102 TYR cc_start: 0.9030 (t80) cc_final: 0.8820 (t80) REVERT: C 139 TYR cc_start: 0.7020 (OUTLIER) cc_final: 0.6318 (t80) outliers start: 28 outliers final: 17 residues processed: 176 average time/residue: 0.1939 time to fit residues: 52.7800 Evaluate side-chains 167 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 40 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 chunk 106 optimal weight: 10.0000 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 30.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11735 Z= 0.200 Angle : 0.668 12.205 15804 Z= 0.331 Chirality : 0.043 0.436 1759 Planarity : 0.003 0.042 2011 Dihedral : 7.500 170.543 1601 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.88 % Allowed : 21.58 % Favored : 76.54 % 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 (0.23), residues: 1411 helix: 0.52 (0.22), residues: 556 sheet: 0.51 (0.34), residues: 259 loop : -0.91 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 289 HIS 0.009 0.001 HIS C 5 PHE 0.019 0.001 PHE B 429 TYR 0.014 0.001 TYR A 373 ARG 0.004 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: A 476 MET cc_start: 0.8613 (ttt) cc_final: 0.8338 (tmm) REVERT: A 567 MET cc_start: 0.9275 (mmm) cc_final: 0.8884 (mmm) REVERT: A 671 GLU cc_start: 0.8630 (pm20) cc_final: 0.8410 (pm20) REVERT: B 311 ASP cc_start: 0.8449 (t0) cc_final: 0.8229 (t0) REVERT: B 362 ILE cc_start: 0.9418 (mm) cc_final: 0.9098 (tp) REVERT: B 385 ASP cc_start: 0.8855 (t0) cc_final: 0.8447 (p0) REVERT: B 513 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7536 (mtm) REVERT: B 553 MET cc_start: 0.9028 (tmm) cc_final: 0.8599 (ppp) REVERT: B 602 MET cc_start: 0.8736 (tpp) cc_final: 0.8225 (tpp) REVERT: B 627 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8442 (pm20) REVERT: B 668 PHE cc_start: 0.8566 (m-80) cc_final: 0.8357 (m-10) REVERT: B 681 TYR cc_start: 0.8769 (m-10) cc_final: 0.8394 (m-80) REVERT: C 40 PHE cc_start: 0.9106 (p90) cc_final: 0.8823 (p90) REVERT: C 45 MET cc_start: 0.9072 (mpp) cc_final: 0.8655 (mpp) REVERT: C 75 GLU cc_start: 0.9056 (pp20) cc_final: 0.8342 (mp0) REVERT: C 84 MET cc_start: 0.8511 (tpp) cc_final: 0.8275 (tpp) REVERT: C 95 ASP cc_start: 0.9163 (m-30) cc_final: 0.8946 (m-30) REVERT: C 102 TYR cc_start: 0.9092 (t80) cc_final: 0.8874 (t80) REVERT: C 139 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.6418 (t80) REVERT: C 143 ASP cc_start: 0.9642 (m-30) cc_final: 0.9395 (p0) outliers start: 24 outliers final: 18 residues processed: 179 average time/residue: 0.1890 time to fit residues: 52.3905 Evaluate side-chains 171 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 1.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 129 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 8.9990 chunk 113 optimal weight: 6.9990 chunk 118 optimal weight: 9.9990 chunk 82 optimal weight: 0.2980 chunk 132 optimal weight: 9.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11735 Z= 0.214 Angle : 0.702 15.821 15804 Z= 0.346 Chirality : 0.043 0.247 1759 Planarity : 0.003 0.042 2011 Dihedral : 7.568 171.406 1601 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.19 % Allowed : 21.50 % Favored : 76.31 % 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: -0.17 (0.23), residues: 1411 helix: 0.52 (0.23), residues: 553 sheet: 0.54 (0.34), residues: 259 loop : -0.95 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 598 HIS 0.010 0.001 HIS C 5 PHE 0.026 0.002 PHE B 32 TYR 0.016 0.001 TYR A 457 ARG 0.004 0.000 ARG B 679 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: A 476 MET cc_start: 0.8642 (ttt) cc_final: 0.8347 (tmm) REVERT: A 567 MET cc_start: 0.9308 (mmm) cc_final: 0.8954 (mmm) REVERT: B 311 ASP cc_start: 0.8460 (t0) cc_final: 0.8227 (t0) REVERT: B 362 ILE cc_start: 0.9417 (mm) cc_final: 0.9110 (tp) REVERT: B 385 ASP cc_start: 0.8871 (t0) cc_final: 0.8455 (p0) REVERT: B 466 MET cc_start: 0.8790 (tpp) cc_final: 0.8562 (mmm) REVERT: B 513 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7622 (mtm) REVERT: B 553 MET cc_start: 0.9000 (tmm) cc_final: 0.8580 (ppp) REVERT: B 602 MET cc_start: 0.8765 (tpp) cc_final: 0.8282 (tpp) REVERT: B 681 TYR cc_start: 0.8797 (m-10) cc_final: 0.8419 (m-80) REVERT: C 45 MET cc_start: 0.9048 (mpp) cc_final: 0.8672 (mpp) REVERT: C 58 LYS cc_start: 0.9416 (tttt) cc_final: 0.9103 (tppt) REVERT: C 95 ASP cc_start: 0.9103 (m-30) cc_final: 0.8872 (m-30) REVERT: C 143 ASP cc_start: 0.9642 (m-30) cc_final: 0.9389 (p0) outliers start: 28 outliers final: 23 residues processed: 172 average time/residue: 0.1928 time to fit residues: 51.4915 Evaluate side-chains 170 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 145 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 596 TYR Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11735 Z= 0.197 Angle : 0.730 14.581 15804 Z= 0.363 Chirality : 0.043 0.226 1759 Planarity : 0.004 0.050 2011 Dihedral : 7.532 170.795 1601 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.11 % Allowed : 22.36 % Favored : 75.53 % 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: -0.32 (0.23), residues: 1411 helix: 0.34 (0.22), residues: 550 sheet: 0.57 (0.34), residues: 259 loop : -1.03 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 598 HIS 0.009 0.001 HIS C 5 PHE 0.021 0.001 PHE C 154 TYR 0.015 0.001 TYR A 457 ARG 0.016 0.000 ARG B 679 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.8631 (OUTLIER) cc_final: 0.8359 (pm20) REVERT: A 363 MET cc_start: 0.8498 (ppp) cc_final: 0.8246 (ppp) REVERT: A 476 MET cc_start: 0.8619 (ttt) cc_final: 0.8356 (tmm) REVERT: A 523 GLN cc_start: 0.8370 (mt0) cc_final: 0.8014 (mt0) REVERT: A 567 MET cc_start: 0.9344 (mmm) cc_final: 0.9000 (mmm) REVERT: B 311 ASP cc_start: 0.8433 (t0) cc_final: 0.8207 (t0) REVERT: B 362 ILE cc_start: 0.9398 (mm) cc_final: 0.9121 (tp) REVERT: B 385 ASP cc_start: 0.8851 (t0) cc_final: 0.8458 (p0) REVERT: B 484 TYR cc_start: 0.8105 (m-10) cc_final: 0.7712 (m-80) REVERT: B 513 MET cc_start: 0.8165 (OUTLIER) cc_final: 0.7697 (mtm) REVERT: B 553 MET cc_start: 0.9003 (tmm) cc_final: 0.8582 (ppp) REVERT: B 602 MET cc_start: 0.8761 (tpp) cc_final: 0.8286 (tpp) REVERT: C 45 MET cc_start: 0.9049 (mpp) cc_final: 0.8664 (mpp) REVERT: C 75 GLU cc_start: 0.9090 (pp20) cc_final: 0.8300 (mp0) REVERT: C 84 MET cc_start: 0.8545 (tpp) cc_final: 0.8198 (tpp) REVERT: C 95 ASP cc_start: 0.9052 (m-30) cc_final: 0.8803 (m-30) REVERT: C 139 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6540 (t80) REVERT: C 143 ASP cc_start: 0.9641 (m-30) cc_final: 0.9385 (p0) outliers start: 27 outliers final: 21 residues processed: 181 average time/residue: 0.1795 time to fit residues: 50.8431 Evaluate side-chains 175 residues out of total 1281 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 151 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 459 THR Chi-restraints excluded: chain A residue 587 SER Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 126 ILE Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 513 MET Chi-restraints excluded: chain B residue 521 CYS Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 664 LEU Chi-restraints excluded: chain B residue 678 ASN Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 70 ASN Chi-restraints excluded: chain C residue 139 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 0.0000 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.0060 chunk 111 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 114 optimal weight: 0.1980 chunk 14 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.066448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.052084 restraints weight = 50061.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.054131 restraints weight = 28279.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.055554 restraints weight = 19061.111| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11735 Z= 0.164 Angle : 0.747 18.704 15804 Z= 0.362 Chirality : 0.043 0.231 1759 Planarity : 0.004 0.042 2011 Dihedral : 7.457 169.650 1601 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.72 % Allowed : 22.99 % Favored : 75.29 % 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: -0.30 (0.23), residues: 1411 helix: 0.32 (0.23), residues: 550 sheet: 0.68 (0.33), residues: 272 loop : -1.06 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 598 HIS 0.009 0.001 HIS C 5 PHE 0.023 0.001 PHE C 154 TYR 0.018 0.001 TYR A 373 ARG 0.014 0.000 ARG B 679 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2223.01 seconds wall clock time: 41 minutes 54.72 seconds (2514.72 seconds total)